A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | ||
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1 | tool_name | citation_key | link_source | doi_manuscript | heatmaps_clustering_genes | pca_mds | volcano_maplot | singlegene_plot | differential_expression | pathway_analysis | id_conversion | complex_models | external_apis | input_formats | feat_sample_filtering | tx_level_analysis | report_generation | state_saving | support_bioc_formats | software_packaged | bioconductor_pkg | deploy_info | demo_available | batch_effect_correction | software_license | software_language | misc_info | |
2 | 3D RNA-seq | Guo2019 | https://github.com/wyguo/ThreeDRNAseq | https://doi.org/10.1101/656686 | yes | yes | yes | yes | yes | yes (plots only) | yes | matrices/tables | low expressed genes | yes | yes (Rmd) | yes (package, docker) | yes | https://ics.hutton.ac.uk/3drnaseq | yes | GPL-3.0 | R | alternative splicing and isoform switch; video tutorial available | ||||||
3 | ABioTrans | Yutong2019 | https://github.com/buithuytien/ABioTrans | https://doi.org/10.1101/616300 | yes | yes | yes | yes | yes | matrices/tables | low expressed genes | app | yes | no | not specified | R | ||||||||||||
4 | ASAP | Gardeux2017 | https://github.com/DeplanckeLab/ASAP | https://doi.org/10.1093/bioinformatics/btx337 | yes | yes | yes | yes | yes | yes | links to ENSEMBL, amiGO | matrices/tables | low expressed genes, variable genes | yes (login required) | app | https://asap.epfl.ch | yes | GPL-3.0 | R, python, Java | focus on single cell data as well; video tutorial available | ||||||||
5 | DEApp | Li2017a | https://github.com/yan-cri/DEApp | https://doi.org/10.1186/s13029-017-0063-4 | yes | yes | yes | yes | matrices/tables | low expressed genes | app | https://yanli.shinyapps.io/DEApp/ | no | GPL-2.0 | R | |||||||||||||
6 | DEBrowser | Kucukural2019 | https://github.com/UMMS-Biocore/debrowser | https://doi.org/10.1186/s12864-018-5362-x | yes | yes | yes | yes | yes | yes | yes | matrices/tables | low expressed genes, sample filtering | no (output from modules provided) | yes (package) | yes | yes | GPL-3.0 | R | modular design | ||||||||
7 | Degust | https://github.com/drpowell/degust | yes | yes | yes | yes | yes | yes (display only) | yes | matrices/tables | low expressed genes | R code | app | yes | http://degust.erc.monash.edu/degust/compare.html?code=example | GPL-3.0 | JavaScript, python | video tutorial available | ||||||||||
8 | DEIVA | Harshbarger2017 | https://github.com/Hypercubed/DEIVA | https://doi.org/10.1186/s12864-016-3396-5 | yes | matrices/tables | app | yes | MIT | JavaScript | ||||||||||||||||||
9 | DEvis | Price2019 | https://github.com/price0416/Devis | https://doi.org/10.1186/s12859-019-2702-z | yes | yes | yes | yes | yes | yes | yes | matrices/tables | low expressed genes | yes | LGPL-3.0 | R | available on CRAN | |||||||||||
10 | DrEdGE | Tintori2020 | https://github.com/ptgolden/dredge | https://doi.org/10.1093/bioinformatics/btz972 | yes | yes | yes | yes | HGNC, MGI, Wormmine | matrices/tables | app | yes | http://dredge.bio.unc.edu/human-neuronal-tissue, http://dredge.bio.unc.edu/mouse-embryonic-tissue/, http://dredge.bio.unc.edu/c-elegans-timecourse/ | AGPL-3.0 | JavaScript, R | deployment-oriented, video tutorial available, svg diagrams for expoloration | ||||||||||||
11 | Glimma | Su2017a | https://github.com/Shians/Glimma | https://doi.org/10.1093/bioinformatics/btx094 | yes | yes | yes | r objects | standalone html page | yes | yes (package) | yes | LGPL-3.0 | R, JavaScript | easy to insert output in report-like HTML documents | |||||||||||||
12 | IDEA | Zhao2018 | https://github.com/likelet/IDEA | https://doi.org/10.1101/360461 | yes | yes | yes | yes | yes | matrices/tables | yes (Rmd) | app | yes | http://renlab.org:3838/IDEA/ | MIT | R | inclusion of different DE methods | |||||||||||
13 | ideal | Marini2020 | https://github.com/federicomarini/ideal | https://doi.org/10.1101/2020.01.10.901652 | yes | yes | yes | yes | yes | yes | yes | links to NCBI, ENSEMBL, amiGO | matrices/tables, r objects | low expressed genes, sample filtering | yes(Rmd), with preview | yes | DESeqDataSet, DESeqResults, SummarizedExperiment | yes (package, conda) | yes | yes | http://shiny.imbei.uni-mainz.de:3838/ideal | MIT | R | rintrojs-based interactive tours (for learning-by-doing), extensive use case documentation | ||||
14 | IDEAMEX | Jimenez-Jacinto2019 | https://github.com/leticiaVega/IDEAMEX | https://doi.org/10.3389/fgene.2019.00279 | yes | yes | yes | yes | yes | yes | matrices/tables | low expressed genes | server | http://www.uusmb.unam.mx/ideamex/ | not specified | apache, php, R | ||||||||||||
15 | iDEP | Ge2018a | https://github.com/iDEP-SDSU/idep/ | https://doi.org/10.1186/s12859-018-2486-6 | yes | yes | yes | yes | yes | yes | yes | yes | KEGG, StringDB | matrices/tables | low expressed genes | app | yes | http://ge-lab.org/idep/ | not specified | R | deployment requires large databases to be downloaded | |||||||
16 | iGeak | Choi2019 | https://sites.google.com/view/iGEAK | https://doi.org/10.1186/s12864-019-5548-x | yes | yes | yes | yes | yes | yes | yes | matrices/tables | low expressed genes | app, standalone | yes | GPL-3.0 | R, JavaScript | standalone version also includes browser | ||||||||||
17 | IRIS-EDA | Monier2018 | https://github.com/btmonier/iris | https://doi.org/10.1371/journal.pcbi.1006792 | yes | yes | yes | yes | yes | matrices/tables | low expressed genes | app | http://bmbl.sdstate.edu/IRIS/ | GPL-3.0 | R | support for preparing GEO metadata | ||||||||||||
18 | MicroScope | Khomtchouk2016a | https://github.com/Bohdan-Khomtchouk/Microscope | https://doi.org/10.1186/s12859-016-1260-x | yes | yes | yes | yes | matrices/tables | app | http://microscopebioinformatics.org/ | GPL-3.0 | R | could be used for different tabular data | ||||||||||||||
19 | pcaExplorer | Marini2019 | https://github.com/federicomarini/pcaExplorer | https://doi.org/10.1186/s12859-019-2879-1 | yes | yes | yes | yes | yes | matrices/tables, r objects | sample filtering | yes(Rmd), with preview | yes | DESeqDataSet, DESeqTransform | yes (package, conda) | yes | yes | http://shiny.imbei.uni-mainz.de:3838/pcaExplorer | MIT | R | focused on the exploratory data analysis step | |||||||
20 | PIVOT | Zhu2018 | https://github.com/qinzhu/PIVOT | https://doi.org/10.1186/s12859-017-1994-0 | yes | yes | yes | yes | yes | yes | yes | yes | matrices/tables, app state | low expressed genes, sample filtering | yes(Rmd), with preview | yes | yes (package, docker) | yes | GPL-2.0 | R | support for project management and single cell data | |||||||
21 | shinyNGS | https://github.com/pinin4fjords/shinyngs | yes | yes | yes | yes | yes | yes | links to ENSEMBL | serialized r object | low expressed genes, sample filtering | SummarizedExperiment | yes (package) | yes | https://pinin4fjords.shinyapps.io/shinyngs_example/ | AGPL-3.0 | R | focused on the post-analysis exploration | ||||||||||
22 | START App | Nelson2016 | https://github.com/jminnier/STARTapp | https://doi.org/10.1093/bioinformatics/btw624 | yes | yes | yes | yes | yes | matrices/tables, app state | low expressed genes | yes | app | yes | https://kcvi.shinyapps.io/START/ | GPL-3.0 | R | custom objects used for state saving and loading | ||||||||||
23 | systemPipeR | Backman2016 | https://github.com/tgirke/systemPipeR | https://doi.org/10.1186/s12859-016-1241-0 | yes | yes | raw fastq data | yes (Rmd) | yes (package) | yes | Artistic-2.0 | R | not directly comparable as it focuses more on the processing pipeline | |||||||||||||||
24 | TCC-GUI | Su2019 | https://github.com/swsoyee/TCC-GUI | https://doi.org/10.1186/s13104-019-4179-2 | yes | yes | yes | yes | yes | matrices/tables | low expressed genes | yes (Rmd) | app | https://infinityloop.shinyapps.io/TCC-GUI/ | MIT | R | revolving around TCC as alternative method for normalization | |||||||||||
25 | TRAPR | Lim2017 | http://www.snubi.org/software/trapr | https://doi.org/10.5808/GI.2017.15.1.51 | yes | yes | yes | yes | matrices/tables | low expressed genes, variable genes | yes (package) | not specified | R | |||||||||||||||
26 | ViDGER | Mcdermaid2018 | https://github.com/btmonier/vidger | https://doi.org/10.1093/bib/bby067 | yes | yes | yes | yes | r objects | yes | yes | yes | GPL-2.0 | R | does not generate plots interactively | |||||||||||||
27 | VIPER | Cornwell2018 | https://bitbucket.org/cfce/viper/ | https://doi.org/10.1186/s12859-018-2139-9 | yes | yes | yes | yes | yes | yes | yes | raw fastq data | low expressed genes | yes | snakemake pipeline | yes | yes | GPL | python | full pipeline, based on snakemake | ||||||||
28 | VisRseq | Younesy2015 | https://visrsoftware.github.io | https://doi.org/10.1186/1471-2105-16-S11-S2 | yes | yes | yes | yes | yes | yes | matrices/tables | low expressed genes, sample filtering | app | not specified | R, Java | focused on the creation of apps based on the provided components; video tutorials available | ||||||||||||
29 | WIlsON | Schultheis2018 | https://github.molgen.mpg.de/loosolab/wilson-apps | https://doi.org/10.1093/bioinformatics/bty711 | yes | yes | yes | yes | CLARION file | low expressed genes, sample filtering | CLARION | app, docker | yes | http://loosolab.mpi-bn.mpg.de/apps/wilson/ | MIT | R | requires explicitly the CLARION format | |||||||||||
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