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>.
Last updated
bedtoolsgenomeinterval-arithmeticcpp
10.87 score 95 stars 2 dependents 306 scripts 3.4k 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.
Last updated
singlecellannotationsequencingmicroarraygeneexpressionassign-identitiesclustersmarker-genesrna-seqsingle-cell-rna-seq
9.24 score 125 stars 390 scripts 472 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.
Last updated
ggplot2ggplot2-geomvisualization
6.30 score 16 stars 63 scripts 279 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.
Last updated
multiplecomparisonrnaseqsinglecellsequencingcoverageepitranscriptomicsfeatureextractionannotationalignmentbioconductor-packagerna-seq-analysissingle-cell-analysissingle-cell-rna-seqcurlbzip2xz-utilszlib
5.78 score 10 stars 6 scripts 334 downloadscpp11bigwig - 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.
Last updated
cpp
5.10 score 3 stars 3 dependents 3 scripts 3.1k downloads