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derfinder:Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.
Maintained by Leonardo Collado-Torres. Last updated 4 months ago.
differentialexpressionsequencingrnaseqchipseqdifferentialpeakcallingsoftwareimmunooncologycoverageannotation-agnosticbioconductorderfinder
42 stars 10.03 score 78 scripts 6 dependentsbioc
recount:Explore and download data from the recount project
Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
Maintained by Leonardo Collado-Torres. Last updated 4 months ago.
coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount
41 stars 9.57 score 498 scripts 3 dependentsbioc
recount3:Explore and download data from the recount3 project
The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.
Maintained by Leonardo Collado-Torres. Last updated 4 months ago.
coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportannotation-agnosticbioconductorcountderfinderexongenehumanilluminajunctionmouserecountrecount3
33 stars 8.03 score 216 scripts