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tool_namecitation_keylink_sourcedoi_manuscript
heatmaps_clustering_genes
pca_mds
volcano_maplot
singlegene_plot
differential_expression
pathway_analysis
id_conversion
complex_models
external_apisinput_formatsfeat_sample_filtering
tx_level_analysis
report_generationstate_savingsupport_bioc_formats
software_packaged
bioconductor_pkg
deploy_infodemo_available
batch_effect_correction
software_license
software_language
misc_info
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3D RNA-seqGuo2019https://github.com/wyguo/ThreeDRNAseqhttps://doi.org/10.1101/656686yesyesyesyesyesyes (plots only)yesmatrices/tableslow expressed genesyesyes (Rmd)yes (package, docker)yeshttps://ics.hutton.ac.uk/3drnaseqyesGPL-3.0Ralternative splicing and isoform switch; video tutorial available
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ABioTransYutong2019https://github.com/buithuytien/ABioTranshttps://doi.org/10.1101/616300yesyesyesyesyesmatrices/tableslow expressed genesappyesnonot specifiedR
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ASAPGardeux2017https://github.com/DeplanckeLab/ASAPhttps://doi.org/10.1093/bioinformatics/btx337yesyesyesyesyesyeslinks to ENSEMBL, amiGOmatrices/tables
low expressed genes, variable genes
yes (login required)apphttps://asap.epfl.chyesGPL-3.0R, python, Javafocus on single cell data as well; video tutorial available
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DEAppLi2017ahttps://github.com/yan-cri/DEApphttps://doi.org/10.1186/s13029-017-0063-4yesyesyesyesmatrices/tableslow expressed genesapphttps://yanli.shinyapps.io/DEApp/noGPL-2.0R
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DEBrowserKucukural2019https://github.com/UMMS-Biocore/debrowserhttps://doi.org/10.1186/s12864-018-5362-xyesyesyesyesyesyesyesmatrices/tables
low expressed genes, sample filtering
no (output from modules provided)
yes (package)yesyesGPL-3.0Rmodular design
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Degusthttps://github.com/drpowell/degustyesyesyesyesyes
yes (display only)
yesmatrices/tableslow expressed genesR codeappyeshttp://degust.erc.monash.edu/degust/compare.html?code=exampleGPL-3.0JavaScript, pythonvideo tutorial available
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DEIVAHarshbarger2017https://github.com/Hypercubed/DEIVAhttps://doi.org/10.1186/s12864-016-3396-5yesmatrices/tablesappyesMITJavaScript
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DEvisPrice2019https://github.com/price0416/Devishttps://doi.org/10.1186/s12859-019-2702-zyesyesyesyesyesyesyesmatrices/tableslow expressed genesyesLGPL-3.0Ravailable on CRAN
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DrEdGETintori2020https://github.com/ptgolden/dredgehttps://doi.org/10.1093/bioinformatics/btz972yesyesyesyesHGNC, MGI, Wormminematrices/tablesappyes
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-3.0JavaScript, Rdeployment-oriented, video tutorial available, svg diagrams for expoloration
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GlimmaSu2017ahttps://github.com/Shians/Glimmahttps://doi.org/10.1093/bioinformatics/btx094yesyesyesr objectsstandalone html pageyesyes (package)yesLGPL-3.0R, JavaScripteasy to insert output in report-like HTML documents
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IDEAZhao2018https://github.com/likelet/IDEAhttps://doi.org/10.1101/360461yesyesyesyesyesmatrices/tablesyes (Rmd)appyeshttp://renlab.org:3838/IDEA/MITRinclusion of different DE methods
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idealMarini2020https://github.com/federicomarini/idealhttps://doi.org/10.1101/2020.01.10.901652yesyesyesyesyesyesyes
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)
yesyeshttp://shiny.imbei.uni-mainz.de:3838/idealMITR
rintrojs-based interactive tours (for learning-by-doing), extensive use case documentation
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IDEAMEXJimenez-Jacinto2019https://github.com/leticiaVega/IDEAMEXhttps://doi.org/10.3389/fgene.2019.00279yesyesyesyesyesyesmatrices/tableslow expressed genesserverhttp://www.uusmb.unam.mx/ideamex/not specifiedapache, php, R
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iDEPGe2018ahttps://github.com/iDEP-SDSU/idep/https://doi.org/10.1186/s12859-018-2486-6yesyesyesyesyesyesyesyesKEGG, StringDBmatrices/tableslow expressed genesappyeshttp://ge-lab.org/idep/not specifiedRdeployment requires large databases to be downloaded
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iGeakChoi2019https://sites.google.com/view/iGEAKhttps://doi.org/10.1186/s12864-019-5548-xyesyesyesyesyesyesyesmatrices/tableslow expressed genesapp, standaloneyesGPL-3.0R, JavaScriptstandalone version also includes browser
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IRIS-EDAMonier2018https://github.com/btmonier/irishttps://doi.org/10.1371/journal.pcbi.1006792yesyesyesyesyesmatrices/tableslow expressed genesapphttp://bmbl.sdstate.edu/IRIS/GPL-3.0Rsupport for preparing GEO metadata
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MicroScopeKhomtchouk2016ahttps://github.com/Bohdan-Khomtchouk/Microscopehttps://doi.org/10.1186/s12859-016-1260-xyesyesyesyesmatrices/tablesapphttp://microscopebioinformatics.org/GPL-3.0Rcould be used for different tabular data
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pcaExplorerMarini2019https://github.com/federicomarini/pcaExplorerhttps://doi.org/10.1186/s12859-019-2879-1yesyesyesyesyes
matrices/tables, r objects
sample filteringyes(Rmd), with previewyes
DESeqDataSet, DESeqTransform
yes (package, conda)
yesyeshttp://shiny.imbei.uni-mainz.de:3838/pcaExplorerMITRfocused on the exploratory data analysis step
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PIVOTZhu2018https://github.com/qinzhu/PIVOThttps://doi.org/10.1186/s12859-017-1994-0yesyesyesyesyesyesyesyes
matrices/tables, app state
low expressed genes, sample filtering
yes(Rmd), with previewyes
yes (package, docker)
yesGPL-2.0Rsupport for project management and single cell data
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shinyNGShttps://github.com/pinin4fjords/shinyngsyesyesyesyesyesyeslinks to ENSEMBL
serialized r object
low expressed genes, sample filtering
SummarizedExperimentyes (package)yeshttps://pinin4fjords.shinyapps.io/shinyngs_example/AGPL-3.0Rfocused on the post-analysis exploration
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START AppNelson2016https://github.com/jminnier/STARTapphttps://doi.org/10.1093/bioinformatics/btw624yesyesyesyesyes
matrices/tables, app state
low expressed genesyesappyeshttps://kcvi.shinyapps.io/START/GPL-3.0Rcustom objects used for state saving and loading
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systemPipeRBackman2016https://github.com/tgirke/systemPipeRhttps://doi.org/10.1186/s12859-016-1241-0yesyesraw fastq datayes (Rmd)yes (package)yesArtistic-2.0Rnot directly comparable as it focuses more on the processing pipeline
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TCC-GUISu2019https://github.com/swsoyee/TCC-GUIhttps://doi.org/10.1186/s13104-019-4179-2yesyesyesyesyesmatrices/tableslow expressed genesyes (Rmd)apphttps://infinityloop.shinyapps.io/TCC-GUI/MITRrevolving around TCC as alternative method for normalization
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TRAPRLim2017http://www.snubi.org/software/traprhttps://doi.org/10.5808/GI.2017.15.1.51yesyesyesyesmatrices/tables
low expressed genes, variable genes
yes (package)not specifiedR
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ViDGERMcdermaid2018https://github.com/btmonier/vidgerhttps://doi.org/10.1093/bib/bby067yesyesyesyesr objectsyesyesyesGPL-2.0Rdoes not generate plots interactively
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VIPERCornwell2018https://bitbucket.org/cfce/viper/https://doi.org/10.1186/s12859-018-2139-9yesyesyesyesyesyesyesraw fastq datalow expressed genesyes
snakemake pipeline
yesyesGPLpythonfull pipeline, based on snakemake
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VisRseqYounesy2015https://visrsoftware.github.iohttps://doi.org/10.1186/1471-2105-16-S11-S2yesyesyesyesyesyesmatrices/tables
low expressed genes, sample filtering
appnot specifiedR, Java
focused on the creation of apps based on the provided components; video tutorials available
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WIlsONSchultheis2018https://github.molgen.mpg.de/loosolab/wilson-appshttps://doi.org/10.1093/bioinformatics/bty711yesyesyesyesCLARION file
low expressed genes, sample filtering
CLARIONapp, dockeryeshttp://loosolab.mpi-bn.mpg.de/apps/wilson/MITRrequires explicitly the CLARION format
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