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Tools Table

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Name
Platform
DOIs
Citations
License
Categories
ACTINNPython10.1093/bioinformatics/btz592, 10.1101/532093195GPL-3.0Classification
ACTIONC++/R/MATLAB10.1038/s41467-018-03933-2, 10.1101/08127351-Clustering, Dimensionality Reduction, Gene Networks
ACTIONetR/C++10.1038/s41467-020-18416-6, 10.1101/74633954GPL-2.0-or-laterClassification, Clustering, Dimensionality Reduction, Gene Sets, Integration, Normalisation, Visualisation
ACTIVAPython10.1093/bioinformatics/btac095, 10.1101/2021.01.28.42872528MITSimulation
ADCPython10.1371/journal.pcbi.10095484-Gene Networks
ADClustPython10.1093/bib/bbac172, 10.1101/2021.12.19.47333423-Clustering, Dimensionality Reduction
ADImputeR10.1101/611517, 10.1371/journal.pcbi.100984917GPL-3.0Imputation
AE-TPGGPython10.1007/s11704-022-2011-y8-Dimensionality Reduction
AGImputePython10.1093/bioinformatics/btae0689-Imputation
ALRAR10.1038/s41467-021-27729-z, 10.1101/397588269MITImputation
ANSPython/R10.1101/2023.09.20.5581142MITGene Sets
APLR/Python10.1016/j.jmb.2022.167525, 10.1101/2020.10.23.35209618GPL-3.0Gene Sets, Marker Genes, Visualisation
ASAPR/Python10.1093/bioinformatics/btx337, 10.1093/nar/gkaa412, 10.1101/096222139GPL-3.0Clustering, Differential Expression, Gene Filtering, Interactive, Normalisation, Visualisation
ASTKPython/R10.1002/aisy.202300594, 10.1101/2023.01.03.5224705BSD-3-ClauseAlternative Splicing, Gene Sets
ASURATR10.1093/bioinformatics/btac541, 10.1101/2021.06.09.4477315GPL-3.0Clustering, Gene Sets, Visualisation
ATAXICR10.1155/2022/41067360-Perturbations
AUCellR10.1038/nmeth.4463, 10.1101/1445014711CustomGene Networks, Interactive, Visualisation
AWGANPython10.1093/bioinformatics/btac427, 10.1101/2021.11.08.46778116MITIntegration
AlakazamR/C++10.1093/bioinformatics/btv359781AGPL-3.0Immune, Visualisation
AltAnalyzePython10.1038/nature19348, 10.1093/nar/gkz789, 10.1101/412080526Apache-2.0Alternative Splicing, Cell Cycle, Classification, Clustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Gene Networks, Gene Sets, Interactive, Marker Genes, Normalisation, Quantification, Visualisation
AlzScPredPython10.1101/2023.07.07.5481712GPL-3.0Classification
AmbientContaminationMetricsPython10.1016/j.isci.2023.107242, 10.1101/2022.10.25.51375812-Quality Control
Anchored-FusionPython10.1016/j.crmeth.2024.1007332GPL-3.0Variants
AnnSqlPython10.1101/2024.11.02.6216760MITClustering, Differential Expression, Dimensionality Reduction, Gene Filtering, Marker Genes, Normalisation, Quality Control, Variable Genes, Visualisation
AnnotatabilityPython10.1038/s43588-024-00721-5, 10.1101/2024.04.06.5883734MITClassification, Dimensionality Reduction
Asc-SeuratR10.1101/2021.03.19.436196, 10.1186/s12859-021-04472-250GPL-3.0Clustering, Differential Expression, Dimensionality Reduction, Integration, Interactive, Ordering, Quality Control, Visualisation
AugurR10.1038/s41587-020-0605-1, 10.1038/s41596-021-00561-x, 10.1101/2019.12.20.884916223MITDimensionality Reduction, Perturbations, Simulation, Variable Genes, Visualisation
AutoClassPython10.1038/s41467-022-29576-y, 10.1101/2020.12.04.41224731GPL-3.0Classification, Imputation
AutoImputePython/R10.1038/s41598-018-34688-x145MITImputation, Normalisation, Variable Genes
AutomaticCellTypeIdentificationR10.1016/j.csbj.2021.10.02755GPL-2.0-or-laterClassification
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