spatialLIBD - spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators.
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homo_sapiens_dataexperimenthubsequencingdatasinglecelldataexpressiondatatissuepackagetypedataspatialdata10xgenomicsbioconductorgolemshinyspatial-transcriptomicsspatialexperimentspatiallibdvisiumdatapkg
11.18 score 114 stars 3 dependents 1.0k scriptsderfinder - 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.
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differentialexpressionsequencingrnaseqchipseqdifferentialpeakcallingsoftwareimmunooncologycoverageannotation-agnosticbioconductorderfinder
10.11 score 45 stars 7 dependents 76 scripts
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.
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coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount
9.55 score 41 stars 4 dependents 588 scripts 1.0k 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.
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coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportannotation-agnosticbioconductorcountderfinderexongenehumanilluminajunctionmouserecountrecount3
8.68 score 40 stars 358 scripts 1.4k downloadsbiocthis - 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.
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softwarereportwritingactionsbioconductorbiocthisgithubstylerusethis
7.76 score 56 stars 1 dependents 5 scripts 1.3k downloadsregionReport - 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.
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differentialexpressionsequencingrnaseqsoftwarevisualizationtranscriptioncoveragereportwritingdifferentialmethylationdifferentialpeakcallingimmunooncologyqualitycontrolbioconductorderfinderdeseq2edgerregionreportrmarkdown
7.15 score 9 stars 52 scripts 674 downloadsderfinderHelper - 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.
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differentialexpressionsequencingrnaseqsoftwareimmunooncologybioconductorderfinder
6.20 score 7 dependents 2 scripts 959 downloadsderfinderData - Processed BigWigs from BrainSpan for examples
Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages.
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experimentdatahomo_sapiens_datarnaseqdatabioconductorderfinderrnaseqdatapkg
4.95 scorederfinderPlot - 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.
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differentialexpressionsequencingrnaseqsoftwarevisualizationimmunooncologybioconductorderfinder
4.30 score 2 stars 9 scripts 710 downloadsrecountWorkflow - recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor
The recount2 resource is composed of over 70,000 uniformly processed human RNA-seq samples spanning TCGA and SRA, including GTEx. The processed data can be accessed via the recount2 website and the recount Bioconductor package. This workflow explains in detail how to use the recount package and how to integrate it with other Bioconductor packages for several analyses that can be carried out with the recount2 resource. In particular, we describe how the coverage count matrices were computed in recount2 as well as different ways of obtaining public metadata, which can facilitate downstream analyses. Step-by-step directions show how to do a gene level differential expression analysis, visualize base-level genome coverage data, and perform an analyses at multiple feature levels. This workflow thus provides further information to understand the data in recount2 and a compendium of R code to use the data.
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workflowresourcequeryingworkflowannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecountrnaseq
3.38 score 4 stars