GenomicAlignments | cran | Package Usage

jimhester/GenomicRanges 📦

* DESCRIPTION

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

vlpb3/faradr

* DESCRIPTION

Size: 4.58 MB - Last synced: 26 days ago - Pushed: over 7 years ago

tidyomics/plyranges

A grammar of genomic data transformation

* DESCRIPTION

Size: 3.25 MB - Last synced: 10 days ago - Pushed: 24 days ago

Bioconductor/BiocParallel

Bioconductor facilities for parallel evaluation

* DESCRIPTION

Size: 1.17 MB - Last synced: 4 days ago - Pushed: 4 days ago

ataudt/aneufinder

Find CNVs in single cell sequencing data.

* DESCRIPTION

Size: 35.9 MB - Last synced: 12 days ago - Pushed: about 1 year ago

MalteThodberg/CAGEfightR

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

>= 1.22.1 DESCRIPTION

Size: 13.5 MB - Last synced: 10 days ago - Pushed: over 2 years ago

Allows general set comparisons with a focus on sets of genomic locations (ChIP-seq peaks primarily). The includes standard visualizations such as venn and euler diagrams but more powerfully of genomic signal pulled from bigwig files.

* DESCRIPTION

Size: 61 MB - Last synced: 16 days ago - Pushed: 16 days ago

powellgenomicslab/DropletQC

Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data

* DESCRIPTION

Size: 16.7 MB - Last synced: 12 days ago - Pushed: over 2 years ago

colomemaria/epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data

* DESCRIPTION
* DESCRIPTION

Size: 31.2 MB - Last synced: 3 months ago - Pushed: 3 months ago

velocyto-team/velocyto.R

RNA velocity estimation in R

* DESCRIPTION

Size: 1.72 MB - Last synced: 7 months ago - Pushed: 8 months ago

rseng/rsepedia-analysis

Exploring clustering of research software encyclopedia entries

>= 1.14.1 _repos/github/LabTranslationalArchitectomics/riboWaltz/DESCRIPTION
* _repos/github/pmoulos/metaseqR2/DESCRIPTION

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

Bioconductor/GenomicFeatures

Conveniently import and query gene models

>= 1.15.7 DESCRIPTION

Size: 45.7 MB - Last synced: 4 days ago - Pushed: 5 days ago

mskilab-org/RSeqLib

R interface to SeqLib

* DESCRIPTION

Size: 27.2 MB - Last synced: about 2 months ago - Pushed: over 1 year ago

gschofl/porequal

Quality assessment of SAM/BAM-based multiple alignments

* DESCRIPTION

Size: 125 KB - Last synced: about 1 year ago - Pushed: over 9 years ago

lawremi/rtracklayer

R interface to genome annotation files and the UCSC genome browser

>= 1.15.6 DESCRIPTION

Size: 15.7 MB - Last synced: 2 days ago - Pushed: 3 days ago

jimhester/AllelicImbalance 📦

* DESCRIPTION

Size: 21.1 MB - Last synced: about 1 year ago - Pushed: about 9 years ago

SLeviyang/RegressHaplo

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Size: 7.96 MB - Last synced: 7 months ago - Pushed: almost 2 years ago

welch16/ChIPexo

ChIP-Exo is a new techonology for sequencing which obtains a higher accuracy to predict TFBS

>= 1.0.1 DESCRIPTION

Size: 207 MB - Last synced: 5 months ago - Pushed: about 6 years ago

PeeperLab/CopywriteR

DNA copy number detection from off-target sequence data

* DESCRIPTION

Size: 2.62 MB - Last synced: about 2 months ago - Pushed: almost 6 years ago

adeschen/similaRpeak

Bioconductor Package - Metrics to estimate the level of similarity between two ChIP-Seq profiles

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Size: 535 KB - Last synced: 6 months ago - Pushed: about 2 years ago

Bioconductor/LearnBioconductor

Training material for introductory R / Bioconductor courses

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Size: 3.38 MB - Last synced: 4 days ago - Pushed: about 1 year ago

Bioconductor/GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.

* DESCRIPTION

Size: 4.36 MB - Last synced: 3 days ago - Pushed: 4 days 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

NKI-GCF/XenofilteR

Filtering of PDX samples for mouse derived reads

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Size: 290 KB - Last synced: about 1 month ago - Pushed: over 1 year ago

gacatag/IntEREst

IntEREst: Intron Exon Retention Estimator

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Size: 2.83 MB - Last synced: 7 months ago - Pushed: 7 months ago

uzh/ezRun

An R meta-package for the analysis of Next Generation Sequencing data

* DESCRIPTION

Size: 131 MB - Last synced: 1 day ago - Pushed: 1 day ago

fmicompbio/QuasR

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

shortRNAhub/shortRNA

short RNA-seq analysis package

* DESCRIPTION

Size: 1.75 GB - Last synced: 4 months ago - Pushed: 4 months ago

romanhaa/Cerebro

Visualization of scRNA-seq data.

* source/Windows/R-Portable-Win/library/IRanges/DESCRIPTION
* source/macOS/R-Portable-Mac/library/IRanges/DESCRIPTION

Size: 2.99 GB - Last synced: 2 months ago - Pushed: over 1 year ago

AngelCampos/txtools

An R package to process and analyze transcriptomic data

* DESCRIPTION

Size: 12.6 MB - Last synced: 30 days ago - Pushed: about 1 month ago

Bioconductor/GenomeInfoDb

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

* DESCRIPTION

Size: 83 MB - Last synced: 4 days ago - Pushed: 5 days ago

daewoooo/SVbyEye

* DESCRIPTION

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

yingstat/intePareto

Prioritize genes with consistent changes in RNA-Seq and ChIP-Seq data of different histone modifications betweeen different conditions using Pareto optimization

* DESCRIPTION

Size: 1.96 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

ZarnackGroup/BindingSiteFinder

Package for the definition of biniding sites for iCLIP data

* DESCRIPTION

Size: 9.77 MB - Last synced: 4 days ago - Pushed: 5 days ago

bioconductor/BiocParallel

* DESCRIPTION

Size: 775 KB - Last synced: about 1 year ago

jianhong/ChIPpeakAnno

* DESCRIPTION

Size: 66 MB - Last synced: 4 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: 18 days ago - Pushed: 9 months ago

AlexisHardy/DNAModAnnot

R toolbox for DNA Modifications filtering and annotation

* DESCRIPTION

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

js2264/VplotR

R package to easily generate "V-plots" of paired-end sequencing data over regions of interest

* DESCRIPTION

Size: 60.7 MB - Last synced: 3 days ago - Pushed: 5 months ago

BrendelGroup/TSRchitect

Promoter identification from diverse types of large-scale TSS profiling data

* DESCRIPTION

Size: 99.5 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

junseonghwan/PhylExAnalysis

>= 1.22.1 PhylExR/DESCRIPTION

Size: 15.5 MB - Last synced: 9 months ago - Pushed: about 1 year ago

anilchalisey/chompR

An R-based pipeline to analyse chromatin modification high throughput sequencing data. This pipeline performs quality control of reads, performs peak-calling, differential peak-calling, and pathway enrichment analyses.

* DESCRIPTION

Size: 980 KB - Last synced: about 1 year ago - Pushed: over 5 years ago

rpolicastro/gostripes

Processing of STRIPE-seq Data

* DESCRIPTION

Size: 8.19 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

lawremi/gmapR

An R interface to the GMAP/GSNAP/GSTRUCT suite

>= 1.15.6 DESCRIPTION

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

HHengUG/hatpal

hatpal is an R package for alternative polyadenylation (APA) identification & analysis using 3’ scRNA-seq (10x etc.).

* DESCRIPTION

Size: 63.5 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

LTLA/csaw

Clone of the Bioconductor repository for the csaw package.

* DESCRIPTION

Size: 11.3 MB - Last synced: about 2 months ago - Pushed: 5 months 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

daewoooo/breakpointR

R Package for breakpoint detection in single cell Strand-seq data.

* DESCRIPTION

Size: 2.84 MB - Last synced: 6 days ago - Pushed: about 1 year ago

LuyiTian/scPipe

a pipeline for single cell RNA-seq data analysis

* DESCRIPTION

Size: 156 MB - Last synced: 25 days ago - Pushed: 5 months ago

stianlagstad/chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.

* DESCRIPTION

Size: 2.9 MB - Last synced: 19 days ago - Pushed: 5 months ago

r-pkg-team/r-bioc-rsamtools

r-bioc-rsamtools packaging

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-genomeinfodb

r-bioc-genomeinfodb packaging

* DESCRIPTION

Last synced: about 1 year ago

ETHZ-INS/epiwraps

Wrappers for dealing and plotting with epigenomics data

* DESCRIPTION

Size: 25.9 MB - Last synced: 6 days ago - Pushed: 6 days ago

r-pkg-team/r-bioc-shortread

r-bioc-shortread packaging

>= 1.15.6 DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-genomicfeatures

r-bioc-genomicfeatures packaging

>= 1.15.7 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-biocparallel

r-bioc-biocparallel packaging

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-biovizbase

r-bioc-biovizbase packaging

>= 1.1.16 DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-gviz

r-bioc-gviz packaging

>=1.1.16 DESCRIPTION

Last synced: about 1 year ago

r-pkg-team/r-bioc-iranges

r-bioc-iranges packaging

* DESCRIPTION

Last synced: over 1 year ago

emilygoren/BinQuasi

* DESCRIPTION

Size: 33.5 MB - Last synced: 9 months ago - Pushed: almost 6 years ago

bioWzz/pulseTD_0.1.0

A tool for analyzing the transcription, processing and degradation rates of genes by 4sU-seq(the Metabolic Label 4-thiouridine) data and RNA-seq(RNA sequencing) data. It can not only recognize the transcriptional dynamic rate at the measurement time points,but also obtain continuous changes in transcriptional dynamics. More importantly,it is able to predict the trend of mRNA(Mature RNA) transcription and expression changes in the future. In terms of performance, 'pulseTD' has good robustness and accuracy.

* DESCRIPTION

Size: 4.15 MB - Last synced: 15 days ago - Pushed: almost 5 years ago

Vivianstats/MAAPER

Model-based analysis of APA using 3' end-linked reads

* DESCRIPTION

Size: 192 KB - Last synced: 15 days ago - Pushed: over 2 years ago

kathrynrozengagnon/CLIPflexR

New repo based on clipr from BRC/RU

* DESCRIPTION

Size: 3.77 MB - Last synced: 9 months ago - Pushed: over 1 year ago

Przemol/seqplots_osx

SeqPlots OS X package

* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/BiocParallel/DESCRIPTION
* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/GenomeInfoDb/DESCRIPTION
* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/GenomicRanges/DESCRIPTION
* SeqPlots.app/Contents/Resources/Rbin/Versions/3.2/Resources/library/Rsamtools/DESCRIPTION

Size: 502 MB - Last synced: about 1 year ago - Pushed: over 7 years ago

welch16/ChIPexoQual

A quality control pipeline for ChIP-exo/nexus samples.

>= 1.0.1 DESCRIPTION

Size: 17.9 MB - Last synced: 5 months ago - Pushed: over 4 years ago

NWPU-903PR/m6Aexpress

* DESCRIPTION

Size: 13.6 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

r-pkg-team/r-bioc-genomicfiles

Distributed computing by file or by range

>= 1.7.7 DESCRIPTION

Last synced: over 1 year ago

LabTranslationalArchitectomics/riboWaltz

optimization of ribosome P-site positioning in ribosome profiling data

>= 1.14.1 DESCRIPTION

Size: 39.2 MB - Last synced: about 2 months ago - Pushed: 4 months ago

sheng-liu/SeqData

A data structure and four simple tools build upon it for sequencing data analysis

* DESCRIPTION

Size: 116 MB - Last synced: about 1 year ago - Pushed: over 9 years ago

rocioespci/single

Rpackage for SINGLe (SNIPS in Nanopore reads of Gene Libraries)

* DESCRIPTION

Size: 1.68 MB - Last synced: 7 months ago - Pushed: about 1 year ago

WinterLi1993/RAPIDR Fork of cran/RAPIDR

:exclamation: This is a read-only mirror of the CRAN R package repository. RAPIDR — Reliable Accurate Prenatal non-Invasive Diagnosis R package

* DESCRIPTION

Size: 1.06 MB - Last synced: about 1 year ago - Pushed: over 9 years ago

guillaumecharbonnier/colab-r-libs

A test to see how I could save installation time for R libs each time I start a Colab notebook

* BiocParallel/DESCRIPTION
* GenomeInfoDb/DESCRIPTION
* GenomicRanges/DESCRIPTION
* IRanges/DESCRIPTION

Size: 156 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

elowy01/CoverageView

Bioconductor package

* DESCRIPTION

Size: 2.56 MB - Last synced: 6 months ago - Pushed: about 9 years ago

mskilab-org/gChain

R class for representing composable syntenic mappings between coordinates of 'omes and allowing nimble lift-over of genomic features and signals through these mappings within a GenomicRanges based framework.