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rdata

Data Analysis and Visualization Using R: Course website

readdepth

R package for inferring copy number from read depth

readseq

Java based common sequence file format reader and sequence file manipulation. Most RDP projects require this package.

readthedocs

Documentation for the Google Genomics cookbook.

recurrentmutationstats

This contains code for statistical analysis of recurrent mutations in whole genome sequencing data.

redbiom

Sample search by metadata and features

refgen

A time-saving tool to change the 'defline' of FASTA files for a range of phylogenetic programs e.g. ClustalX, MrBayes, PhyML

refund

:exclamation: This is a read-only mirror of the CRAN R package repository. refund — Regression with Functional Data

refund.wave

Wavelet-based regression for scalar responses and functional predictors.

regeval

A systematic evaluation of high-dimensional, ensemble based regression for exploring large model spaces in microbiome analyses.

region_analysis

A python script used to annotate genomic intervals.

regression-models

Implemented different regression models without using scikit learn functionalities during model building process

reviews

Writing reviews of academic papers

rforproteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

rgithubclient

Making it easier for R to talk to github

rhtslib

R wrapper for htslib for high-throughput sequence analysis

riboprofiling

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/RiboProfiling.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=RiboProfiling.

riesling-pipeline

RIESLING: Super-enhancer identification. (Rapid Identification of EnhancerS LInked to Nearby Genes)

risa

Risa allows to access metadata/data in ISA-tab format and builds Bioconductor data structures. Apart from parsing ISA-tab files, the package also provides functionality to save the ISA-tab dataset, or each of its individual files. Additionally, it is also possible to update assay files. Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into an xcmsSet object (from the xcms R package).

rj

A package for managing r journal metadata

rmarkdown

Dynamic Documents for R

rna-seq-diff-exprn

RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).

rna-seq_course

rnaseqpipeline

bash pipeline for RNAseq data analysis

rols

An R package to query EBI's Ontology Lookup Service (OLS)

rook

Open, Cloud Native, and Universal Distributed Storage

rpackages

R package development - the Leek group way!

rreebes

Reproducible Research in Ecology, Evolution, Behaviour, and Environmental Studies

rsem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

rstudio

RStudio is an integrated development environment (IDE) for R