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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 scriptsbioc
regionReport:Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.
Maintained by Leonardo Collado-Torres. Last updated 3 months ago.
differentialexpressionsequencingrnaseqsoftwarevisualizationtranscriptioncoveragereportwritingdifferentialmethylationdifferentialpeakcallingimmunooncologyqualitycontrolbioconductorderfinderdeseq2edgerregionreportrmarkdown
9 stars 7.22 score 46 scriptsbioc
derfinderHelper:derfinder helper package
Helper package for speeding up the derfinder package when using multiple cores. This package is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel.
Maintained by Leonardo Collado-Torres. Last updated 4 months ago.
differentialexpressionsequencingrnaseqsoftwareimmunooncologybioconductorderfinder
6.20 score 7 dependentsbioc
derfinderPlot:Plotting functions for derfinder
This package provides plotting functions for results from the derfinder package. This helps separate the graphical dependencies required for making these plots from the core functionality of derfinder.
Maintained by Leonardo Collado-Torres. Last updated 4 months ago.
differentialexpressionsequencingrnaseqsoftwarevisualizationimmunooncologybioconductorderfinder
2 stars 5.00 score 5 scripts