recipe bioconductor-genomicalignments

Representation and manipulation of short genomic alignments

Homepage:

https://bioconductor.org/packages/3.14/bioc/html/GenomicAlignments.html

License:

Artistic-2.0

Recipe:

/bioconductor-genomicalignments/meta.yaml

Links:

biotools: genomicalignments

Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

package bioconductor-genomicalignments

Versions:

1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.1-0, 

1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.1-0,  1.20.0-0,  1.18.1-0,  1.18.0-0,  1.16.0-0,  1.14.1-0,  1.14.0-0,  1.12.2-0,  1.10.0-0,  1.8.4-0,  1.6.3-1,  1.6.3-0,  1.6.1-0,  1.6.0-0

Depends:

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-biostrings >=2.62.0,<2.63.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rsamtools >=2.10.0,<2.11.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• r-base >=4.1,<4.2.0a0

Required By:

• bioconductor-cssq

• bioconductor-prebs

• bioconductor-crisprvariants

• bioconductor-cager

• bioconductor-msgbsr

• bioconductor-scate

• bioconductor-biovizbase

• bioconductor-vasp

• bioconductor-strandcheckr

• bioconductor-guideseq

• bioconductor-metagene2

• bioconductor-diffbind

• bioconductor-alpinedata

• bioconductor-repitools

• bioconductor-aspediafi

• bioconductor-brgenomics

• bioconductor-pram

• bioconductor-hireadsprocessor

• bioconductor-customprodb

• bioconductor-igvr

• bioconductor-customprodb

• bioconductor-methylpipe

• bioconductor-rqc

• r-ggcoverage

• bioconductor-scatedata

• bioconductor-proactiv

• bioconductor-chipexoqual

• arriba

• bioconductor-tapseq

• bioconductor-fraser

• bioconductor-leebamviews

• bioconductor-aneufinder

• r-alakazam

• bioconductor-atacseqqc

• bioconductor-ribodipa

• bioconductor-sgseq

• bioconductor-allelicimbalance

• bioconductor-pics

• bioconductor-nadfinder

• bioconductor-alpine

• bioconductor-chipqc

• bioconductor-seqsetvis

• bioconductor-gviz

• bioconductor-atena

• bioconductor-genogam

• bioconductor-inspect

• bioconductor-chimeraviz

• bioconductor-soggi

• bioconductor-aspli

• bioconductor-exomepeak2

• bioconductor-chromstar

• bioconductor-funchip

• bioconductor-tcseq

• r-rapidr

• bioconductor-shortread

• bioconductor-breakpointr

• riboseqc

• bioconductor-tsrchitect

• bioconductor-ribosomeprofilingqc

• bioconductor-basicstarrseq

• r-nanopore

• bioconductor-htseqgenie

• bioconductor-rnamodr

• bioconductor-damefinder

• bioconductor-greylistchip

• bioconductor-cagefightr

• bioconductor-metaseqr2

• bioconductor-mosaics

• bioconductor-umi4cats

• bioconductor-ggbio

• bioconductor-plyranges

• bioconductor-degnorm

• bioconductor-orfik

• bioconductor-vplotr

• bioconductor-copywriter

• bioconductor-trackviewer

• bioconductor-gcapc

• bioconductor-consensusde

• bioconductor-basic4cseq

• bioconductor-bambu

• bioconductor-descan2

• bioconductor-genomation

• bioconductor-icetea

• bioconductor-splinter

• orfquant

• ribowaltz

• bioconductor-easyrnaseq

• bioconductor-gmoviz

• bioconductor-grohmm

• bioconductor-roar

• bioconductor-cner

• bioconductor-contibait

• bioconductor-baalchip

• bioconductor-coverageview

• bioconductor-helloranges

• bioconductor-metagene

• bioconductor-scruff

• r-exomedepth

• bioconductor-genomicfiles

• bioconductor-ramwas

• bioconductor-apalyzer

• bioconductor-madseq

• bioconductor-gmapr

• bioconductor-transcriptr

• bioconductor-rtracklayer

• bioconductor-interest

• bioconductor-chippeakanno

• bioconductor-srnadiff

• bioconductor-recoup

• bioconductor-riboprofiling

• bioconductor-imas

• bioconductor-tarseqqc

• bioconductor-rcade

• bioconductor-mdts

• bioconductor-macpet

• bioconductor-derfinder

• bioconductor-splicinggraphs

• bioconductor-ularcirc

• bioconductor-spiky

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-genomicalignments

and update with:

conda update bioconductor-genomicalignments

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-genomicalignments:<tag>

(see bioconductor-genomicalignments/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-genomicalignments/README.html)