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Tools Table

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Name
Platform
DOIs
Citations
License
Categories
acordeR10.1038/s41467-022-29497-w, 10.1101/2021.05.07.44184113GPL-3.0Alternative Splicing, Differential Expression, Visualisation
ACTINNPython10.1093/bioinformatics/btz592, 10.1101/532093178GPL-3.0Classification
ACTIONC++/R/MATLAB10.1038/s41467-018-03933-2, 10.1101/08127346-Clustering, Dimensionality Reduction, Gene Networks
ACTIONetR/C++10.1038/s41467-020-18416-6, 10.1101/74633948GPL-2.0-or-laterClassification, Clustering, Dimensionality Reduction, Gene Sets, Integration, Normalisation, Visualisation
ACTIVAPython10.1093/bioinformatics/btac095, 10.1101/2021.01.28.42872524MITSimulation
activeSVCPython10.1038/s43588-022-00263-8, 10.1101/2021.06.15.44847820MITMarker Genes, Variable Genes
ADCPython10.1371/journal.pcbi.10095484-Gene Networks
ADClustPython10.1093/bib/bbac172, 10.1101/2021.12.19.47333417-Clustering, Dimensionality Reduction
ADImputeR10.1101/611517, 10.1371/journal.pcbi.100984914GPL-3.0Imputation
adoboPython10.1093/bioinformatics/btaa26934GPL-3.0Cell Cycle, Classification, Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Imputation, Normalisation, Quality Control, Visualisation
adverSCarialR-MITClassification
AE-TPGGPython10.1007/s11704-022-2011-y6-Dimensionality Reduction
aggregateBioVarR10.1093/bioinformatics/btab33723GPL-3.0Quantification
AGImputePython10.1093/bioinformatics/btae0689-Imputation
airpartR-GPL-2.0Alternative Splicing, Quality Control, Visualisation
aLDGRarxiv/2203.019900GPL-3.0Gene Networks
alevin-fryRust10.1038/s41592-022-01408-3, 10.1101/2021.06.29.45037773BSD-3-ClauseAlignment, Quantification, UMIs
alevinQCR-MITInteractive, Visualisation
ALRAR10.1038/s41467-021-27729-z, 10.1101/397588237MITImputation
AltAnalyzePython10.1038/nature19348, 10.1093/nar/gkz789, 10.1101/412080517Apache-2.0Alternative Splicing, Cell Cycle, Classification, Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Networks, Gene Sets, Interactive, Marker Genes, Normalisation, Quantification, Visualisation
AlzScPredPython10.1101/2023.07.07.5481711GPL-3.0Classification
AmbientContaminationMetricsPython10.1016/j.isci.2023.107242, 10.1101/2022.10.25.5137589-Quality Control
anchorPython10.1016/j.molcel.2017.06.003165BSD-3-ClauseModality
Anchored-FusionPython10.1016/j.crmeth.2024.1007331GPL-3.0Variants
AnnotatabilityPython10.1101/2024.04.06.5883731MITClassification, Dimensionality Reduction
AnnSqlPython10.1101/2024.11.02.6216760MITClustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Marker Genes, Normalisation, Quality Control, Variable Genes, Visualisation
ANSPython/R10.1101/2023.09.20.5581141MITGene Sets
anticor_featuresPython10.1038/s41467-023-43406-9, 10.1101/2022.12.05.5191617AGPL-3.0Variable Genes
APLR/Python10.1016/j.jmb.2022.167525, 10.1101/2020.10.23.35209617GPL-3.0Gene Sets, Marker Genes, Visualisation
ASAPR/Python10.1093/bioinformatics/btx337, 10.1093/nar/gkaa412, 10.1101/096222134GPL-3.0Clustering, Differential Expression, Gene Filtering, Interactive, Normalisation, Visualisation
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