edgeR - Empirical Analysis of Digital Gene Expression Data in R

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.

Last updated 26 days ago

geneexpressiontranscriptionalternativesplicingcoveragedifferentialexpressiondifferentialsplicingdifferentialmethylationgenesetenrichmentpathwaysgeneticsdnamethylationbayesianclusteringchipseqregressiontimecoursesequencingrnaseqbatcheffectsagenormalizationqualitycontrolmultiplecomparisonbiomedicalinformaticscellbiologyfunctionalgenomicsepigeneticsimmunooncologysystemsbiologytranscriptomicssinglecell

13.47 score 252 packages 16k scripts 43k downloads

scider - Spatial cell-type inter-correlation by density in R

scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.

Last updated 26 days ago

spatialtranscriptomics

4.90 score 2 stars 3 scripts 113 downloads