link to webpage

parent_organization_id

Defining_Citation

Related_Disease

Additional_Resource_Types

Related_Application

Funding_Information

Publication_Link

Twitter_Handle

Alternate_URLs

Terms_Of_Use_URLs

Supporting_Agency

relationship_strings

resources_scr_ids

nif-0000-00023

Neuroshare - Open data specifications and software for neurophysiology

software toolkit,software library,software resource

Neuroshare.org

data management, development, interoperability software, software

http://neuroshare.sourceforge.net/index.shtml

nif-0000-00023

software resource

ncdfFlow: A package that provides ncdf based storage for flow cytometry data

software package, mac os x, unix/linux, windows, r, flow cytometry

http://www.bioconductor.org/packages/release/bioc/html/ncdfFlow.html

Artistic License, v2

is_listed_by|has_parent_organization

SCR_002250|SCR_006442

data analysis software,software application,data processing software,software resource,alignment software,image analysis software

bisulfite sequence, read-level methylation, bisulfite sequence reads alignment,

https://github.com/BenLangmead/bsmooth-align

Free, Available for download, Freely available

https://help.github.com/articles/github-terms-of-service/

GPL v3, Apache License

software resource,software application

mac os x, sequence, trace file

http://nucleobytes.com/index.php/4peaks

SCR_011508,SCR_011698

PMID:20028542

software resource,data processing software,data analysis software,software application

sequence analysis software, transcription factor binding site, chip-seq, blind deconvolution, transcription binding, bio.tools

http://crab.rutgers.edu/~dslun/csdeconv/index.html

Public, Open source

http://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-12-r142

https://bio.tools/csdeconv

OMICS_00436, biotools:csdeconv

is_listed_by|is_listed_by|is_listed_by|has_parent_organization|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_011508|SCR_011698

PMID:22445902

software resource

Tablet - Next Generation Sequence Assembly Visualization

next generation sequence, assembly, alignment

http://bioinf.scri.ac.uk/tablet/

Acknowledgement requested

is_listed_by|has_parent_organization

SCR_002250|SCR_011324

software resource,software application

gene, genetic, genomic

http://www.people.fas.harvard.edu/~junliu/em/em.htm

Steve Qin, (email: qin (at) stat.harvard.edu), Jun S Liu (email: jliu (at) stat.harvard.edu)

is_listed_by|has_parent_organization

SCR_013155|SCR_011273

software resource

GenomicRanges - Representation and manipulation of genomic intervals

GenomicRanges

genomic interval

http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html

Artistic License, v2

OMICS_01161, SCR_018096, SCR_018096

is_used_by|is_listed_by|has_parent_organization

SCR_016948|SCR_002250|SCR_006442

PMID:23620357

software resource

standalone software

https://github.com/brendanofallon/SNPSVM/

SCR_013141,SCR_000996

PMID:24600385

software toolkit,data analysis software,software application,data processing software,software resource

NIPY Diffusion Imaging Analysis, Diffusion Imaging In Python

MRI, magnetic resonance, diffusion data analysis, diffusion MRI data,diffusion MRI data analysis,

https://dipy.org/

Free, Available for download, Freely available

https://sources.debian.org/src/python-dipy/, http://www.nitrc.org/projects/dipy, http://elef.soic.indiana.edu/, https://github.com/nipy/dipy_web,

http://nipy.org/dipy/

BSD License, Creative Commons Attribution 3.0 License

is_listed_by|is_listed_by|has_parent_organization|has_parent_organization

SCR_003430|SCR_006638|SCR_013141|SCR_000996

SCR_006442,SCR_011603

PMID:22748112

standalone software,software resource,software application

ReadqPCR - Read qPCR data

standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools

http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html

http://www.biomedcentral.com/1471-2164/13/296

https://bio.tools/readqpcr

OMICS_03936, biotools:readqpcr

GNU Lesser General Public License v3

is_listed_by|is_listed_by|is_listed_by|has_parent_organization|has_parent_organization

SCR_002250|SCR_006638|SCR_014695|SCR_006442|SCR_011603

PMID:23634845

software resource

standalone software, windows

http://sourceforge.net/projects/spdesigner/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

PMID:23935067

sequence analysis software,data analysis software,software application,data processing software,software resource

BlackOPs: RNA-Seq Variant Blacklist Tool

rna seq, false positive, genome editing, rna editing, mismapped reads

http://sourceforge.net/projects/rnaseqvariantbl/

Free, Available for download, Freely available

Acknowledgement requested

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

SciRes_000168

software resource,data acquisition software,data processing software,software application

PATCHMASTER

HEKA , HEKA amplifiers and data acquisition hardware support,

http://www.heka.com/products/products_main.html#soft_pm

SciRes_000168

Commercially available. Software updates are available free of charge.

nif-0000-31399

portal,topical portal,software resource,data or information resource

RCSB Software Tools

Information Portal, Biological Macromolecular Structure, RCSB, RCSB software tools, data extraction, format conversion, data parsing, data management, visualization, pdbx/mmcif, pdbx, mmcif

http://sw-tools.pdb.org/index.html

Free, Available for download, Freely available

nif-0000-31399

http://sw-tools.pdb.org/license.txt

is_listed_by|is_related_to|has_parent_organization

SCR_014079|SCR_005085|SCR_012820

PMID:22160811

software resource

Graphical User-friendly Analysis of Relaxation Dispersion Data

standalone software, matlab, bio.tools

https://code.google.com/p/guardd/

GNU General Public License

https://bio.tools/guardd

OMICS_04020, biotools:guardd

is_listed_by|is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_005786

PMID:16118183

software resource

mac os x, unix/linux, windows, c, c++, perl

http://code.google.com/p/apsampler/

is_listed_by|has_parent_organization

SCR_002250|SCR_005786

data visualization software,data processing software,software resource,software application

visualize meshes,color, opacity, smoothing, down sampling, type of representation,

http://www.nitrc.org/projects/meshmetric3d/

Free, Available for download, Freely available

3D Slicer License

SCR_005786,SCR_011241

PMID:22789590

software resource

unix/linux, mac os x, windows

https://code.google.com/p/cbrowse/

GNU General Public License

is_listed_by|has_parent_organization|has_parent_organization

SCR_002250|SCR_005786|SCR_011241

PMID:24728858

standalone software,software resource,software application

java, 3 prime utr, rna sequence, change point model, detecting 3-prime UTR changes, RNA-Seq

http://utr.sourceforge.net/

Free, Available for download, Freely available

uses|is_listed_by|has_parent_organization

SCR_021974|SCR_002250|SCR_004365

SCR_006442,SCR_004201

software resource

flowCL - Semantic labelling of flow cytometric cell populations

software package, mac os x, unix/linux, windows, r, flow cytometry

http://www.bioconductor.org/packages/release/bioc/html/flowCL.html

Artistic License, v2

is_listed_by|has_parent_organization|has_parent_organization

SCR_002250|SCR_006442|SCR_004201

PMID:20519285

software resource

http://sourceforge.net/projects/cg-pipeline/

GNU General Public License

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

software resource

Basic Alignment Tool for MAny Nucleotides

http://sourceforge.net/projects/batman-seq/

is_listed_by|is_hosted_by

SCR_002250|SCR_004365

software resource

http://sourceforge.net/projects/imethy/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

software resource

c++, command-line, pcr, primer, aligned sequence, degenerate primer

http://sourceforge.net/projects/dprimer/

GNU General Public License, v3

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

SCR_006442,SCR_004201

PMID:25600947

software resource

flowBin - Combining multitube flow cytometry data by binning

software package, flow cytometry data, r, cell based assay, expression

http://www.bioconductor.org/packages/release/bioc/html/flowBin.html

Artistic License, v2

NIBIB | R01EB008400, Canadian Cancer Society | , Michael Smith Foundation for Health Research | , International Society for the Advancement of Cytometry |

is_listed_by|is_related_to|has_parent_organization|has_parent_organization

SCR_002250|SCR_003005|SCR_006442|SCR_004201

PMID:24681904

sequence analysis software,data analysis software,software application,data processing software,software resource

CorMut - Detect the correlated mutations based on selection pressure

sequencing, correlated mutation, selection pressure, r, bio.tools

http://bioconductor.org/packages/release/bioc/html/CorMut.html

THIS RESOURCE IS NO LONGER IN SERVICE

https://bio.tools/cormut

OMICS_03636, biotools:cormut

GNU General Public License v2

is_listed_by|is_listed_by|is_listed_by|is_related_to|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_003005|SCR_006442

software resource,data processing software,data analysis software,software application

ChIPmeta with HHM

chip-chip, chip-seq, ChIP-chip and ChIP-seq datasets analysis,

http://sourceforge.net/projects/chipmeta/

Free, Available for download, Freely available

PMID:20472541

software resource

Fast and Accurate Classification of Sequences

unix/linux, sequence, bio.tools

https://github.com/SciLifeLab/facs

https://bio.tools/facs

OMICS_02147, biotools:facs

is_listed_by|is_listed_by|is_listed_by|is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_002630|SCR_014695|SCR_006638|SCR_024411|SCR_014078

software resource,data processing software,data analysis software,software application

differential expression, rna-seq, sequencing

http://www.bioconductor.org/packages/release/bioc/html/metaSeq.html

Artistic License, v2

is_listed_by|has_parent_organization

SCR_002250|SCR_006442

SCR_004365,SCR_011529

PMID:22689759

software application,data processing software,software resource,alignment software,image analysis software

Dissect: DIScovery of Structural Events Containing Transcripts, DIScovery of Structural Events Containing Transcripts

Structural events containing transcripts, transcriptome-to-genome alignment, identify and characterize transcriptomic events, bio.tools

http://dissect-trans.sourceforge.net/Home

https://bio.tools/dissect

OMICS_01346, biotools:dissect

is_listed_by|is_listed_by|is_listed_by|has_parent_organization|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_004365|SCR_011529

PMID:22570408

software resource,data processing software,data analysis software,software application

FusionAnalyser

gene fusion, rna-seq, paired-end rna-seq data, fusion event, bio.tools

http://www.ngsbicocca.org/html/fusion_analyser.html

THIS RESOURCE IS NO LONGER IN SERVICE

https://bio.tools/fusionanalyser

OMICS_01347, biotools:fusionanalyser

Apache License

is_listed_by|is_listed_by|is_listed_by

SCR_002250|SCR_014695|SCR_006638

DOI:10.1101/011650

sequence analysis software,data analysis software,software application,data processing software,software resource

fusion gene, known fusion gene, translocation, chimera, rna-seq data, hiseq, solexa, bio.tools

http://code.google.com/p/fusioncatcher/

Free, Available for download, Freely available

https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md, https://bio.tools/fusioncatcher

OMICS_01348, biotools:fusioncatcher

is_listed_by|is_listed_by|is_listed_by

SCR_002250|SCR_006638|SCR_014695

PMID:19477992

software resource,data processing software,data analysis software,software application

Geometric Analysis of Structural Variants

paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools

http://code.google.com/p/gasv/

Free, Available for download, Freely available

Burroughs Wellcome Fund | , Department of Defense Breast Cancer Research | , ADVANCE Program at Brown University | , NSF | 0548311

http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv

https://code.google.com/projecthosting/terms.html

OMICS_01352, biotools:gasv

is_listed_by|is_listed_by|is_listed_by|is_related_to|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_005259|SCR_000957

PMID:22574135

software resource,data processing software,data analysis software,software application

GPU-based HOmology Search Tool for Metagenomics, ghostm: GPU-based HOmology Search Tool for Metagenomics

homology search, next-generation sequencers short reads, detect remote homologs,

https://code.google.com/p/ghostm/

Free, Available for download, Freely available,

is_listed_by|is_listed_by

SCR_002250|SCR_005786

PMID:16621010

software resource,software toolkit

custom built multiphoton microscopes suite,

http://physics.ucsd.edu/neurophysics/links.html

THIS RESOURCE IS NO LONGER IN SERVICE

http://www.nitrc.org/projects/mpscope

is_listed_by|has_parent_organization

SCR_003430|SCR_016626

PMID:22745232

software resource

nFuse: Discovery of Complex Genomic Rearrangements in Cancer

cancer, genomics

https://code.google.com/p/nfuse/

GNU General Public License, v3

is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_005786|SCR_011529

PMID:10534053

software toolkit,software application,image processing software,data processing software,software resource,image analysis software

Medical Image Registration ToolKit

image processing,processing and analyzing imaging data,adult and neonatal brain MR image registration,

http://www.doc.ic.ac.uk/~dr/software/

Free, Available for download, Freely available

https://biomedia.doc.ic.ac.uk/software/irtk/, https://github.com/BioMedIA/MIRTK

has_parent_organization

PMID:24278254

software toolkit,software library,software resource

PD5: A Software Library for the Development of Primer Design Applications

c++, primer design, primer, pcr, software repository, library

https://code.google.com/p/primer-design/

GNU General Public License v3

is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_005786|SCR_000949

PMID:23531354

software resource

genome, allele, copy number, bam, unix, r, bio.tools

http://patchwork.r-forge.r-project.org/

https://bio.tools/patchwork

OMICS_02118, biotools:patchwork

is_listed_by|is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_011751

PMID:23734724

Normal, Tumor, Cancer

software resource

single-nucleotide variant, sequenced genome, genotype, genome

http://www.iro.umontreal.ca/~csuros/quadgt/

New BSD License

Terry Fox Research Institute | , Canadian Institutes for Health Research | , Canada National Sciences and Engineering Research Council |

is_listed_by|has_parent_organization

SCR_002250|SCR_011685

SCR_006442,SCR_004984

PMID:24681907

software resource

VariantAnnotation - Annotation of Genetic Variants

VariantAnnotation

annotation, genetic variant, data import, genetics, high throughput sequencing, snp, sequencing

http://www.bioconductor.org/packages/2.12/bioc/html/VariantAnnotation.html

Artistic License, v2

is_listed_by|is_related_to|has_parent_organization|has_parent_organization

SCR_002250|SCR_003005|SCR_006442|SCR_004984

PMID:22946927

software resource

Recalibrating Quality Of Nucleotides

preprocessing, quality control, sequencing

http://www.bioconductor.org/packages/release/bioc/html/ReQON.html

GNU General Public License, v2

is_listed_by|has_parent_organization

SCR_002250|SCR_006442

software resource

SnowsShoes-FTD

software, bioinformatics, transcriptome sequences, data, LINUX, node, free

http://www.mayo.edu/research/departments-divisions/department-health-sciences-research/division-biomedical-statistics-informatics/software/bioinformatics-software-packages

THIS RESOURCE IS NO LONGER IN SERVICE

GNU General Public License, published by the Free Software Foundation

is_listed_by|has_parent_organization

SCR_002250|SCR_011383

SCR_006442,SCR_011618

software resource

timecourse - Statistical Analysis for Developmental Microarray Time Course Data

microarray, differential expression, time course, bio.tools

http://www.bioconductor.org/packages/release/bioc/html/timecourse.html

GNU Lesser General Public License

https://bio.tools/timecourse

OMICS_01980, biotools:timecourse

is_listed_by|is_listed_by|is_listed_by|is_related_to|has_parent_organization|has_parent_organization

SCR_002250|SCR_006638|SCR_014695|SCR_003005|SCR_006442|SCR_011618

PMID:23409703

software resource

software, resource, open license, DNA sequencing, genome, transcripts, RNA, oligonucleotide

http://soap.genomics.org.cn/soapfuse.html

THIS RESOURCE IS NO LONGER IN SERVICE

http://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-2-r12

http://groups.google.com/group/bgi-soap

is_listed_by|is_listed_by|is_listed_by

SCR_002250|SCR_004365|SCR_000689

PMID:24123671

software resource

software, open source, free, RNA, sequencing, data, computing, research, analysis, rna-seq, candidate regions, bio.tools

http://soap.genomics.org.cn/SOAPfusion.html

THIS RESOURCE IS NO LONGER IN SERVICE

Guangdong Innovative Research Team Program | , General Research Fund of the Hong Kong Government |

https://bio.tools/soapfusion

OMICS_01358, biotools:soapfusion

is_listed_by|is_listed_by|is_listed_by|is_listed_by

SCR_002250|SCR_000689|SCR_014695|SCR_006638

software resource

VectorValuedHistogramNormalizer

magnetic resonance, mri, standardization, histogram, intensity

http://www.nitrc.org/projects/vvhistomatch/

is_listed_by|is_listed_by|is_related_to|has_parent_organization

SCR_003430|SCR_001976|SCR_002347|SCR_011639

nif-0000-23328

source code,software resource,software application,simulation software

fluid simulation, lagrangian particle fluid, linux

https://simtk.org/home/aspf

nif-0000-23328

is_listed_by|is_listed_by

SCR_001976|SCR_002680

PMID:22772728

software resource

pLink (pFind Studio), pLink2, pLink,

mass spectrometry, proteomics,pFind Studio, bio.tools

http://pfind.ict.ac.cn/software/pLink/index.html

https://bio.tools/pLink-2

OMICS_02404, biotools:pLink-2

is_listed_by|is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_012797

software resource

TIGR Spotfinder

http://www.tm4.org/spotfinder.html

is_listed_by|has_parent_organization

SCR_002250|SCR_003040

software resource

Generalized Ontological Algorithmic Logical Invariants Extractor, Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE)

gene ontology, statistical analysis, time-course

http://bioinformatics.nyu.edu/Projects/GOALIE/

THIS RESOURCE IS NO LONGER IN SERVICE

is_listed_by|has_parent_organization

SCR_006941|SCR_005697

PMID:24423623

software resource

standalone software, illumina, roche, life technologies, python

http://sourceforge.net/projects/abmining/

GNU General Public License

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

PMID:19154595

software resource

Signaling Networks Analysis and Visualization

standalone software, bio.tools

https://code.google.com/p/snavi/

GNU General Public License

https://bio.tools/snavi

OMICS_04122, biotools:snavi

is_listed_by|is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_005786

PMID:24916385

standalone software,software resource,software application

peak annotation, peaks probabilistic identifications,

https://mzmatch.sourceforge.net/MetAssign.php

Free, Freely available

http://mzmatch.sourceforge.net/

is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_004365|SCR_011646

software resource

applet, mac os x, unix/linux, windows, java

http://jchempaint.github.io/

GNU Lesser General Public License

https://github.com/JChemPaint/jchempaint/, http://jchempaint.github.com

PMID:16870995

software resource

standalone software, java

http://sourceforge.net/projects/sirnarules/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

web service,software resource,data access protocol

primer, real-time pcr, primer design

http://www.autoprime.de/AutoPrimeWeb

THIS RESOURCE IS NO LONGER IN SERVICE

http://genomebiology.com/2004/5/5/P11

Acknowledgement requested

GNU General Public License, v3

is_listed_by|has_parent_organization

SCR_002250|SCR_012942

software resource

RmiR.Hs.miRNA: Various databases of microRNA Targets

software package, unix/linux, mac os x, windows, r, annotation data, custom db schema, mirna

http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html

Artistic License, v2

is_listed_by|is_related_to|has_parent_organization

SCR_002250|SCR_003005|SCR_006442

PMID:22046244

software resource

standalone software

http://sourceforge.net/projects/mysirna/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

PMID:19210774

software resource

taxonomy, genomic fragment, metagenome

http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/99-tacoa?highlight=WyJ0YWNvYSJd

is_listed_by|has_parent_organization

SCR_002250|SCR_011116

PMID:20172941

software resource

Treephyler: fast taxonomic profiling of metagenomes

metagenome, perl, nucleotide, protein, next-generation sequencing

http://www.gobics.de/fabian/treephyler.php

Acknowledgement requested, Free, Public

nif-0000-00067

PMID:15055395

software toolkit,software resource

data storage, metadata, neuroinformatics

https://www.neuroscholar.org/neuroscholar_demo.html

Free, Available for download, Freely available

http://www.neuroscholar.org

nif-0000-00067

has_parent_organization

PMID:24398007

software resource

standalone software, python

http://sourceforge.net/projects/dtailor/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

PMID:21562803

software resource

neuronal circuit, neuron tracing, branch structure, automated tracing

http://neurogeometry.net/

NINDS | NS063494

https://bpb-us-w2.wpmucdn.com/sites.northeastern.edu/dist/9/312/files/2020/09/User-Guide-V-4-0.pdf

is_related_to|is_related_to|has_parent_organization

SCR_008955|SCR_008995|SCR_011468

PMID:22464129

software resource

standalone software

http://biolemmatizer.sourceforge.net/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

SCR_006442,SCR_004960

PMID:23097420

software resource

AffyRNADegradation

rna degradation, gene expression, microarray, preprocessing, affymetrix, rna, bio.tools

http://www.bioconductor.org/packages/release/bioc/html/AffyRNADegradation.html

GNU General Public License, v2

https://bio.tools/affyrnadegradation

OMICS_01975, biotools:affyrnadegradation

is_listed_by|is_listed_by|is_listed_by|has_parent_organization|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_006442|SCR_004960

PMID:19429689

software resource,software application,simulation software

metagenomic open reading frame, tool, resource, protein, genes, DNA, phyologenetic origin, machine learning, linear discriminates, artificial neural network, computation, scientific computing, fragment

http://orphelia.gobics.de/

THIS RESOURCE IS NO LONGER IN SERVICE

SCR_006442,SCR_004727

PMID:19505942

software resource

ArrayExpress (R)

http://www.bioconductor.org/packages/release/bioc/html/ArrayExpress.html

Artistic License, v2

is_listed_by|is_related_to|has_parent_organization|has_parent_organization

SCR_002250|SCR_002964|SCR_006442|SCR_004727

PMID:23046922

software resource,data processing software,data analysis software,software application

Parallel META, Parallel Meta

data mining, microbial community data, comparative taxonomics, metagenomic analysis, parallel algorithms

http://www.computationalbioenergy.org/parallel-meta.html

THIS RESOURCE IS NO LONGER IN SERVICE

http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-6-S1-S16

software resource,software application

R/ENTROPY_BLOCKER, R/ENTROPY BLOCKER

ENTROPY BLOCKER

gene, genetic, genomic, r, ms-windows, linux

http://wpicr.wpic.pitt.edu/WPICCompGen/blocks.htm

nlx_154300, nlx_154581, SCR_007247, SCR_007247, nlx_154581

Faceted Search Based Ontology Visualizer

software resource

computational neuroscience, magnetic resonance, ontology, functional neuroanatomy, facet, visualization

http://www.nitrc.org/projects/ontologyviz/

3D Slicer License

PMID:23034731

web service,software resource,data access protocol

CovalentDock Cloud

protein ligand covalent docking, ligand, receptor, covalent linkage, data analysis service, bio.tools

http://docking.sce.ntu.edu.sg/

THIS RESOURCE IS NO LONGER IN SERVICE

http://onlinelibrary.wiley.com/doi/10.1002/jcc.23136/abstract;jsessionid=9A6256F1E4443B2BE6BCF43C9D0D4493.f02t02?wol1URL=/doi/10.1002/jcc.23136/abstract&regionCode=US-CA&identityKey=d9260c4d-e5e4-45fc-a0bb-12c4a13ccccc

https://bio.tools/covalentdock_cloud

OMICS_01597, covalentdock_cloud

It is highly recommended to read the Help page before the first use of this web service.

is_listed_by|is_listed_by|is_listed_by

SCR_002250|SCR_014695|SCR_006638

software resource

molecule docking, ligand model, drug design, molecular biology

http://dock.compbio.ucsf.edu/

Available to the research community, Free for the academic community, License fee for industrial organizations, Available for download

is_listed_by|has_parent_organization

SCR_002250|SCR_010605

PMID:24603341

software resource

standalone software, c, matlab

http://sourceforge.net/projects/exomesuite/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

PMID:24093227, PMID:22506599, DOI:10.1089/cmb.2012.0021

software resource,software toolkit

SPAdes Genome Assembler

assembler, single, cell, small, genome, short, read, data

https://cab.spbu.ru/software/spades/

Free, Available for download, Freely available

Government of the Russian Federation | , NCRR | P41 RR024851

https://sources.debian.org/src/spades/

http://bioinf.spbau.ru/spades/

GNU General Public License, v2

is_used_by|is_listed_by|is_listed_by|is_listed_by|is_related_to|is_related_to|has_parent_organization|works_with

SCR_017077|SCR_002250|SCR_006638|SCR_024411|SCR_016992|SCR_016994|SCR_011515|SCR_020125

PMID:30254741

software resource

http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

Free, Freely available

GNU General Public License, v3 or later

is_listed_by|has_parent_organization

SCR_002250|SCR_011106

PMID:22426993

source code,software resource

Weka Nifti-Importer

Nifti-Importer for WEKA

fmri, neuroimaging, java, classifier, regression analysis, classification, pattern

http://www.uni-marburg.de/fb12/kebi/research/software/nifti_importer?language_sync=1

Creative Commons License

has_parent_organization

SCR_006442,SCR_011417

PMID:17496320

software resource

GEOquery - Get data from NCBI Gene Expression Omnibus (GEO)

microarray, bio.tools

http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html

GNU General Public License, v2

https://bio.tools/geoquery, https://sources.debian.org/src/r-bioc-geoquery/

biotools:geoquery, OMICS_01972

is_listed_by|is_listed_by|is_listed_by|is_related_to|is_related_to|has_parent_organization|has_parent_organization

SCR_002250|SCR_014695|SCR_006638|SCR_007303|SCR_016569|SCR_006442|SCR_011417

web service,software resource,data access protocol

image, gene, ontology or annotation browser

http://mor.nlm.nih.gov/perl/gennav.pl

Free for academic use

is_listed_by|is_related_to|has_parent_organization

SCR_006941|SCR_002811|SCR_011446

PMID:21527027

software resource

GISTIC2.0, GISTIC 2.0, GISTIC 2

somatic copy-number alteration, gene

http://www.mmnt.net/db/0/0/ftp-genome.wi.mit.edu/distribution/GISTIC2.0

BROAD INSTITUTE SINGLE USER LICENSE AGREEMENT FOR INTERNAL RESEARCH PURPOSES ONLY, Ftp://ftp-genome.wi.mit.edu/distribution/GISTICv2/LICENSE.txt

is_listed_by|has_parent_organization

SCR_002250|SCR_000977

PMID:20979621, DOI:10.1186/s13059-014-0550-8

software resource,data processing software,data analysis software,software application

gene expression, binomial, differential, negative binomial distribution, bio.tools

http://bioconductor.org/packages/release/bioc/html/DESeq.html

THIS RESOURCE IS NO LONGER IN SERVICE

http://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106

https://bio.tools/deseq, https://sources.debian.org/src/r-bioc-deseq2/

biotools:deseq, OMICS_01306

is_listed_by|is_listed_by|is_listed_by|is_hosted_by

SCR_002250|SCR_006638|SCR_014695|SCR_006442

PMID:23977141

software resource

standalone software, r

http://cran.r-project.org/src/contrib/Archive/postgwas/

is_listed_by|has_parent_organization

SCR_002250|SCR_003005

software toolkit,software library,software resource

covariance, estimation, matlab

https://github.com/atlab/cov-est

has_parent_organization

PMID:24685334

software resource

perl, blast, short sequence, primer, png, png graph

http://sourceforge.net/projects/blastplot/

Open source, Available for download

https://slashdotmedia.com/terms-of-use/ https://slashdotmedia.com/privacy-statement/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

PMID:21515631

software resource,web application

mirna, microrna, next gen sequencing, analysis, next generation, next gen, detection tool, analysis tool

http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php

THIS RESOURCE IS NO LONGER IN SERVICE

http://nar.oxfordjournals.org/content/39/suppl_2/W132

PMID:23047563

data analytics software,software resource,software application

algorithm, copy number, next-generation, reference genome, dataset comparison

http://sourceforge.net/projects/magnolya/

Open source, Available for download

http://bioinformatics.oxfordjournals.org/content/28/24/3195.long

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

PMID:23861572

sequence analysis software,data analysis software,software application,data processing software,software resource

Genome Microsatellite Analyzing Tool, Genome-wide Microsatellite Analyzing Tool (GMATo), Genome-wide Microsatellite Analyzing Tool

simple sequence repeat, ssr, microsatellite, genomic, marker design, sequence analysis software

http://sourceforge.net/projects/gmato/files/?source=navbar

Open source, Free, Available for download

https://slashdotmedia.com/terms-of-use/ https://slashdotmedia.com/privacy-statement/

is_listed_by|has_parent_organization

SCR_002250|SCR_004365

PMID:22336055, DOI:10.1186/1471-2164-13-74

software resource

bioinformatics, simulation, sequencing, dna, rna, empirical models, Python, command-line, user interface, metagenomic, resequencing, bio.tools

http://sourceforge.net/projects/gemsim/

Public, Open Source

https://bio.tools/GemSIM

OMICS_01507, biotools:GemSIM

GNU General Public License version 3.0 (GPLv3)

is_listed_by|is_listed_by|is_listed_by|has_parent_organization|is_required_by

SCR_002250|SCR_006638|SCR_014695|SCR_004365|SCR_002567

PMID:22434876, DOI:10.1093/nar/gks251

software resource

simulation, amplicon, shotgun, genomic sequencing, clinical, metagenomic, transcriptomic and metatranscriptomic

http://sourceforge.net/projects/biogrinder/

Public, Open Source

https://sources.debian.org/src/grinder/

GNU General Public License version 2.0 (GPLv2) Features

is_listed_by|is_listed_by|has_parent_organization

SCR_002250|SCR_006638|SCR_004365

software application,data processing software,software resource,registration software,image analysis software

magnetic resonance

http://www.nitrc.org/projects/cmfreg/

3D Slicer License

nif-0000-00357

Wavelet Analysis of Image Registration

data processing software,software resource,software application,image analysis software

image analysis, cluster group classification, spread group classification, Java, warp, wavelet space triangle analysis

http://www.loni.usc.edu/Software/WAIR

Available for educational and research purposes only

NIBIB|9P41EB015922-15

http://loni.usc.edu/Software/termsofuse.php

nif-0000-00357

http://loni.usc.edu/Software/license.php

is_related_to|has_parent_organization

SCR_001922|SCR_008093

SCR_011403,SCR_011176

PMID:15998470

software resource,web application

term enrichment, gene ontology, gene, microarray, common variable immune deficiency, high-throughput, visualization, database

http://discover.nci.nih.gov/gominer/GoCommandWebInterface.jsp

Free for academic use, Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

NCI|1Z01BC010842-01

http://genomebiology.biomedcentral.com/articles/10.1186/gb-2003-4-4-r28

GO data updates: no fixed update schedule

is_listed_by|is_related_to|is_related_to|has_parent_organization|has_parent_organization

SCR_006941|SCR_002811|SCR_002360|SCR_011403|SCR_011403