valr - Genome Interval Arithmetic
Read and manipulate genome intervals and signals. Provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data. Riemondy et al. (2017) <doi:10.12688/f1000research.11997.1>.
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bedtoolsgenomeinterval-arithmeticcpp
10.45 score 97 stars 2 dependents 389 scripts 1.8k downloadsclustifyr - Classifier for Single-cell RNA-seq Using Cell Clusters
Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.
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singlecellannotationsequencingmicroarraygeneexpressionassign-identitiesclustersmarker-genesrna-seqsingle-cell-rna-seq
9.13 score 127 stars 294 scripts 576 downloadsggtrace - Trace and Highlight Groups of Data Points
Provides 'ggplot2' geoms that allow groups of data points to be outlined or highlighted for emphasis. This is particularly useful when working with dense datasets that are prone to overplotting.
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ggplot2ggplot2-geomvisualization
6.32 score 16 stars 65 scripts 295 downloads
raer - RNA editing tools in R
Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.
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multiplecomparisonrnaseqsinglecellsequencingcoverageepitranscriptomicsfeatureextractionannotationalignmentbioconductor-packagerna-seq-analysissingle-cell-analysissingle-cell-rna-seqcurlbzip2xz-utilszlib
6.04 score 11 stars 7 scripts 428 downloadsclustifyrdatahub - External data sets for clustifyr in ExperimentHub
References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr <https://bioconductor.org/packages/clustifyr> to assign cell type identities.
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singlecelldatasequencingdatamicroarraydataexperimenthubrnaseqdatapackagetypedataexpressiondatarna-seq-analysissingle-cellsingle-cell-rna-seqdatapkg
5.99 score 9 stars 18 scriptscpp11bigwig - Read bigWig and bigBed Files
Read bigWig and bigBed files using "libBigWig" <https://github.com/dpryan79/libBigWig>. Provides lightweight access to the binary bigWig and bigBed formats developed by the UCSC Genome Browser group.
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curlzlibcpp
4.97 score 4 stars 3 dependents 3 scripts 1.7k downloadsraerdata - A collection of datasets for use with raer package
raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided.
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singlecelldatasequencingdatarnaseqdataexperimenthubpackagetypedataexpressiondatadatapkg
3.30 score 4 scripts