BSgenome | cran | Package Usage | Ecosyste.ms: Repos

MeichunCai/KataegisPortal

An R package for detecting and visualizing Kataegis events

* DESCRIPTION

Size: 10.9 MB - Last synced: 7 months ago - Pushed: over 1 year ago

jimhester/GenomicRanges 📦

* DESCRIPTION

Size: 8.35 MB - Last synced: about 1 year ago - Pushed: about 9 years ago

fmicompbio/monaLisa

binned motif enrichment analysis and visualisation

* DESCRIPTION

Size: 44.9 MB - Last synced: 5 days ago - Pushed: 5 days ago

clark-lab-robot/Repitools-git

A git version of our Repitools R package (the R-forge svn version will *always* be more up do date)

* pkg/Repitools/DESCRIPTION
* pkg/Repitools/DESCRIPTION

Size: 3.12 MB - Last synced: 7 months ago - Pushed: almost 13 years ago

Simon-Coetzee/motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.

* DESCRIPTION

Size: 6.86 MB - Last synced: 11 days ago - Pushed: 11 days ago

PhanstielLab/plotgardener

* DESCRIPTION

Size: 126 MB - Last synced: 3 days ago - Pushed: 18 days ago

ErasmusMC-CCBC/katdetectr

An R package for detection, characterization and visualization of kataegis.

>= 1.62.0 DESCRIPTION

Size: 1.3 MB - Last synced: 2 months ago - Pushed: 2 months ago

GreenleafLab/chromVAR

chromatin Variability Across Regions (of the genome!)

* DESCRIPTION

Size: 18.8 MB - Last synced: 3 months ago - Pushed: 6 months ago

griffithlab/GenVisR

Genome data visualizations

* DESCRIPTION

Size: 38 MB - Last synced: 22 days ago - Pushed: 22 days ago

ShixiangWang/sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

* DESCRIPTION

Size: 51 MB - Last synced: 22 days ago - Pushed: about 2 months ago

databio/GenomicDistributions

Calculate and plot distributions of genomic ranges

* DESCRIPTION

Size: 9.27 MB - Last synced: 9 days ago - Pushed: 9 days ago

rseng/rsepedia-analysis

Exploring clustering of research software encyclopedia entries

* _repos/github/RajLabMSSM/echolocatoR/DESCRIPTION
* _repos/github/ShixiangWang/sigminer/DESCRIPTION
* _repos/github/pmoulos/metaseqR2/DESCRIPTION

Size: 433 MB - Last synced: 3 days ago - Pushed: 5 days ago

PeteHaitch/methsim

An R package to simulate DNA methylation data.

* DESCRIPTION

Size: 16.3 MB - Last synced: about 1 year ago - Pushed: almost 8 years ago

Bioconductor/GenomicFeatures

Conveniently import and query gene models

* DESCRIPTION

Size: 45.7 MB - Last synced: 3 days ago - Pushed: 5 days ago

MatthiasLienhard/qsea

QSEA bioconductor package

* DESCRIPTION

Size: 381 KB - Last synced: 7 months ago - Pushed: about 1 year ago

Codezy99/cliProfiler

* DESCRIPTION

Size: 232 KB - Last synced: 5 months ago - Pushed: over 2 years ago

lawremi/rtracklayer

R interface to genome annotation files and the UCSC genome browser

>= 1.33.4 DESCRIPTION

Size: 15.7 MB - Last synced: 2 days ago - Pushed: 2 days ago

gustaveroussy/EaCoN

Easy Copy Number !

* DESCRIPTION

Size: 3.1 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

lianos/seqtools

Utilities to deal with sequencing data

* R/pkg/DESCRIPTION

Size: 430 KB - Last synced: 7 months ago - Pushed: over 9 years ago

wzthu/esATAC

Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis

* DESCRIPTION

Size: 23.9 MB - Last synced: 15 days ago - Pushed: over 1 year ago

khughitt/EuPathDB

EuPathDB recipe for the Bioconductor AnnotationHub

* DESCRIPTION

Size: 3.19 MB - Last synced: 6 months ago - Pushed: 6 months ago

Bioconductor/VariantAnnotation

Annotation of Genetic Variants

>= 1.47.3 DESCRIPTION

Size: 3.67 MB - Last synced: 3 days ago - Pushed: 4 days ago

fmicompbio/eisaR

Exon-Intron Split Analysis (EISA) in R

* DESCRIPTION

Size: 12.3 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.

* DESCRIPTION

Size: 13.3 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

pmoulos/prisma

Automated Polygenic Risk Score modeling and evaluation

* DESCRIPTION

Size: 3.65 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

neurogenomics/MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

* DESCRIPTION

Size: 8.7 MB - Last synced: 3 days ago - Pushed: 4 days ago

Bioconductor/GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

* DESCRIPTION

Size: 83 MB - Last synced: 3 days ago - Pushed: 5 days ago

CompEpigen/scMethrix

An R 📦 for fast and flexible scDNA methylation analysis

* DESCRIPTION

Size: 30.9 MB - Last synced: 8 months ago - Pushed: about 2 years ago

Bioconductor/GenomicAlignments

Representation and manipulation of short genomic alignments

* DESCRIPTION

Size: 6.08 MB - Last synced: 3 days ago - Pushed: 5 days ago

daewoooo/SVbyEye

* DESCRIPTION

Size: 5.42 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

bioconductor/QDNAseq

>= 1.38.0 DESCRIPTION

Size: 772 KB - Last synced: about 1 year ago

jianhong/ChIPpeakAnno

* DESCRIPTION

Size: 66 MB - Last synced: 3 days ago - Pushed: 9 days ago

ohlerlab/RiboseQC

Pipeline for Quality Control of Ribo-Seq data, selection of P-site offsets, and codon usage statistics.

* DESCRIPTION

Size: 23.6 MB - Last synced: 17 days ago - Pushed: 9 months ago

AlexisHardy/DNAModAnnot

R toolbox for DNA Modifications filtering and annotation

>= 1.28.0 DESCRIPTION

Size: 56.2 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

KasperThystrup/circulaR

R package for setting up and performing circRNA analysis from hcimeric read output, generated by the STAR aligner.

>= 1.56.0 DESCRIPTION

Size: 312 KB - Last synced: 12 months ago - Pushed: about 3 years ago

huanyaogao/catalogueR

* DESCRIPTION

Size: 105 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago

chavez-lab/MEDIPS

MEDIPS - MEthylated DNA ImmunoPrecipitation Sequencing analysis

* DESCRIPTION

Size: 11.6 MB - Last synced: 6 months ago - Pushed: about 3 years ago

wzthu/enrichTF

Bioconductor package enrichTF: Transcription Factors Enrichment Analysis

* DESCRIPTION

Size: 1.29 MB - Last synced: 15 days ago - Pushed: about 4 years ago

morrislab/TrackSigFreq

R package for TrackSig and TrackSigFreq

* DESCRIPTION

Size: 459 KB - Last synced: 9 months ago - Pushed: over 1 year ago

cran/sigminer

:exclamation: This is a read-only mirror of the CRAN R package repository. sigminer — Extract, Analyze and Visualize Mutational Signatures for Genomic Variations. Homepage: https://github.com/ShixiangWang/sigminer, https://shixiangwang.github.io/sigminer/, https://shixiangwang.github.io/sigminer-book/ Report bugs for ...

* DESCRIPTION

Size: 14.7 MB - Last synced: 5 months ago - Pushed: 5 months ago

Deisiany/BSgenome.Gmax.NCBI.Gmv40

This package has the full genome sequences for Glycine max as provided by EnsemblPlants, and it intends to facilitate the data analysis for G. max by making its full genome sequences available through BSgenome.

>= 1.63.4 BSgenome.Gmax.NCBI.Gmv40/DESCRIPTION
* BSgenome.Gmax.NCBI.Gmv40/DESCRIPTION

Size: 41 KB - Last synced: 7 months ago - Pushed: almost 2 years ago

Bioconductor/BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs

>= inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION
* inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION
>= inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION
* inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION

Size: 11.3 MB - Last synced: 3 days ago - Pushed: 5 days ago

databio/GenomicDistributionsData

Data for GenomicDistributions R package

* DESCRIPTION

Size: 65.4 KB - Last synced: 12 days ago - Pushed: over 2 years ago

lawremi/gmapR

An R interface to the GMAP/GSNAP/GSTRUCT suite

* DESCRIPTION

Size: 5.89 MB - Last synced: 4 months ago - Pushed: 4 months ago

Nik-Zainal-Group/signature.tools.lib

R package containing useful functions for mutational signature analysis

* DESCRIPTION

Size: 25 MB - Last synced: 28 days ago - Pushed: 28 days ago

sarangian/bulkRNASeqPIPE

Differential Expression Analysis of bulk-RNASeq data

* utility/deaRscripts/DESCRIPTION

Size: 347 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

crisprVerse/crisprDesign

Comprehensive design of CRISPR gRNAs for nucleases and base editors

* DESCRIPTION

Size: 5.84 MB - Last synced: 3 days ago - Pushed: 17 days ago

lianos/GenomicCache

Extensions to Bioconductor GenomicFeatures package. Primarily, this implements a more "Gene Centric" view on the world, as opposed to base GenomicFeature's transcript/exon/cds centric view.

* DESCRIPTION

Size: 239 KB - Last synced: about 1 year ago - Pushed: over 5 years ago

jsemple19/methMatrix

Operations on methylation matrices from dSMF pipeline

* DESCRIPTION

Size: 106 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

VCCRI/Ularcirc

An R-shiny app that provides backsplice and canonical splicing analysis for both circular RNA (circRNA) and parental transcripts

* DESCRIPTION

Size: 54.5 MB - Last synced: about 1 month ago - Pushed: about 2 years ago

mghandi/gkmSVM

gkmSVM R package

* DESCRIPTION

Size: 147 KB - Last synced: 7 months ago - Pushed: over 6 years ago

malnirav/hiAnnotator

Functions for annotating GRanges objects

* DESCRIPTION

Size: 2.13 MB - Last synced: 9 months ago - Pushed: almost 3 years ago

ccagc/QDNAseq

QDNAseq package for Bioconductor

>= 1.38.0 DESCRIPTION

Size: 13.2 MB - Last synced: 4 days ago - Pushed: about 1 year ago

r-pkg-team/r-bioc-genomeinfodb

r-bioc-genomeinfodb packaging

* DESCRIPTION

Last synced: about 1 year ago

r-pkg-team/r-bioc-variantannotation

r-bioc-variantannotation packaging

>= 1.47.3 DESCRIPTION

Last synced: about 1 year ago

r-pkg-team/r-bioc-genomicalignments

r-bioc-genomicalignments packaging

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-bsgenome

r-bioc-bsgenome packaging

>= inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION
* inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION
>= inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION
* inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION

Last synced: about 1 year ago

r-pkg-team/r-bioc-isoformswitchanalyzer

Identify, Annotate and Visualize Alternative Splicing and

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-genomicfeatures

r-bioc-genomicfeatures packaging

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-genomicranges

r-bioc-genomicranges packaging

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-pwmenrich

PWM enrichment analysis

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-biovizbase

r-bioc-biovizbase packaging

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-gviz

r-bioc-gviz packaging

>= 1.33.1 DESCRIPTION

Last synced: about 1 year ago

steverozen/ICAMS

ICAMS: In-depth Characterization and Analysis of Mutational Signatures

* DESCRIPTION

Size: 822 MB - Last synced: 23 days ago - Pushed: 3 months ago

Przemol/seqplots_osx

SeqPlots OS X package

>= SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/BSgenome/pkgtemplates/BSgenome_datapkg/DESCRIPTION
* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/BSgenome/pkgtemplates/BSgenome_datapkg/DESCRIPTION
>= SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/BSgenome/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION
* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/BSgenome/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION
>= 1.13.14 SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/Biostrings/DESCRIPTION
* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/GenomeInfoDb/DESCRIPTION
* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/GenomicAlignments/DESCRIPTION
* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/GenomicRanges/DESCRIPTION