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bioc
DESeq2:Differential gene expression analysis based on the negative binomial distribution
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Maintained by Michael Love. Last updated 25 days ago.
sequencingrnaseqchipseqgeneexpressiontranscriptionnormalizationdifferentialexpressionbayesianregressionprincipalcomponentclusteringimmunooncologyopenblascpp
375 stars 16.11 score 17k scripts 115 dependentsbioc
BiocGenerics:S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructurebioconductor-packagecore-package
12 stars 14.22 score 612 scripts 2.2k dependentsbioc
SingleCellExperiment:S4 Classes for Single Cell Data
Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.
Maintained by Davide Risso. Last updated 24 days ago.
immunooncologydatarepresentationdataimportinfrastructuresinglecell
13.53 score 15k scripts 285 dependentsbioc
OUTRIDER:OUTRIDER - OUTlier in RNA-Seq fInDER
Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results.
Maintained by Christian Mertes. Last updated 5 months ago.
immunooncologyrnaseqtranscriptomicsalignmentsequencinggeneexpressiongeneticscount-datadiagnosticsexpression-analysismendelian-geneticsoutlier-detectionrna-seqopenblascpp
50 stars 9.07 score 110 scripts 1 dependents