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.

Last updated 24 days ago

coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount

9.44 score 40 stars 3 packages 478 scripts 617 downloads

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.

Last updated 24 days ago

differentialexpressionsequencingrnaseqchipseqdifferentialpeakcallingsoftwareimmunooncologycoverageannotation-agnosticbioconductorderfinder

9.07 score 42 stars 6 packages 77 scripts 916 downloads

biocthis - Automate package and project setup for Bioconductor packages

This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.

Last updated 24 days ago

softwarereportwritingactionsbioconductorbiocthisgithubstylerusethis

7.77 score 50 stars 1 packages 4 scripts 509 downloads

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.

Last updated 24 days ago

coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportannotation-agnosticbioconductorcountderfinderexongenehumanilluminajunctionmouserecountrecount3

7.73 score 31 stars 174 scripts 480 downloads

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.

Last updated 24 days ago

differentialexpressionsequencingrnaseqsoftwarevisualizationtranscriptioncoveragereportwritingdifferentialmethylationdifferentialpeakcallingimmunooncologyqualitycontrolbioconductorderfinderdeseq2edgerregionreportrmarkdown

6.90 score 9 stars 44 scripts 306 downloads

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.

Last updated 24 days ago

differentialexpressionsequencingrnaseqsoftwareimmunooncologybioconductorderfinder

6.02 score 7 packages 813 downloads

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.

Last updated 24 days ago

differentialexpressionsequencingrnaseqsoftwarevisualizationimmunooncologybioconductorderfinder

5.00 score 2 stars 5 scripts 270 downloads