gencore_rnaseq
Summary
Coming soon!
Software Packages
bamtools
Version: 2.4.0
Conda Channel: bioconda
Summary:
C++ API & command-line toolkit for working with BAM data
bcftools
Version: 1.3.1
Conda Channel: bioconda
Summary:
Tools for dealing with BCF and VCF files
bedtools
Version: 2.25.0
Conda Channel: bioconda
Summary:
A powerful toolset for genome arithmetic
bioconductor-ballgown
Version: 2.2.0
Conda Channel: bioconda
Summary:
bioconductor-biovizbase
Version: 1.18.0
Conda Channel: bioconda
Summary:
The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.
bioconductor-cummerbund
Version: 2.16.0
Conda Channel: bioconda
Summary:
Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
bioconductor-deseq2
Version: 1.12.4
Conda Channel: bioconda
Summary:
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
bioconductor-edger
Version: 3.14.0
Conda Channel: bioconda
Summary:
Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.
bioconductor-genomicranges
Version: 1.26.1
Conda Channel: bioconda
Summary:
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals. Specialized containers for representing and manipulating short alignments against a reference genome are defined in the GenomicAlignments package.
bioconductor-gviz
Version: 1.16.5
Conda Channel: bioconda
Summary:
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
bioconductor-s4vectors
Version: 0.12.0
Conda Channel: bioconda
Summary:
The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
blat
Version: 35
Conda Channel: bioconda
Summary:
BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.
bowtie2
Version: 2.2.8
Conda Channel: bioconda
Summary:
Fast and sensitive read alignment
cufflinks-patch
Version: 2.2.1
Conda Channel: nyuad-cgsb
Summary:
Transcriptome assembly and differential expression analysis for RNA-Seq
fastqc
Version: 0.11.5
Conda Channel: bioconda
Summary:
A quality control tool for high throughput sequence data.
gatk
Version: 3.6
Conda Channel: bioconda
Summary:
The full Genome Analysis Toolkit (GATK) framework, license restricted.
hisat2
Version: 2.0.4
Conda Channel: bioconda
Summary:
graph-based alignment of next generation sequencing reads to a population of genomes
htseq
Version: 0.6.1.post1
Conda Channel: bioconda
Summary:
A framework to process and analyze data from high-throughput sequencing (HTS) assays
kallisto
Version: 0.43.0
Conda Channel: bioconda
Summary:
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
perl-biox-workflow-plugin-filedetails
Version: 0.11
Conda Channel: bioconda
Summary:
Get metadata for files in directories processed by BioX::Workflow
perl-biox-workflow-plugin-fileexists
Version: 0.13
Conda Channel: bioconda
Summary:
a plugin to BioX::Workflow
perl-biox-workflow
Version: 1.10
Conda Channel: bioconda
Summary:
A very opinionated template based workflow writer.
perl-hpc-runner-command
Version: 3.1.1
Conda Channel: bioconda
Summary:
picard
Version: 2.5.0
Conda Channel: bioconda
Summary:
prinseq
Version: 0.20.4
Conda Channel: bioconda
Summary:
PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data
r-base
Version: 3.3.1
Conda Channel: r
Summary:
r-cairo
Version: latest
Conda Channel: r
Summary:
This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
r-essentials
Version: latest
Conda Channel: r
Summary:
Some essential packages for working with R
samtools
Version: 1.3.1
Conda Channel: bioconda
Summary:
Tools for dealing with SAM, BAM and CRAM files
seqtk
Version: 1.2
Conda Channel: bioconda
Summary:
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
star
Version: 2.5.2a
Conda Channel: bioconda
Summary:
An RNA-seq read aligner.
stringtie
Version: 1.3.0
Conda Channel: bioconda
Summary:
Transcriptome assembly and quantification for RNA-seq
tophat
Version: 2.1.0
Conda Channel: bioconda
Summary:
A spliced read mapper for RNA-Seq
trimmomatic
Version: 0.36
Conda Channel: bioconda
Summary:
Genetic variant annotation and effect prediction toolbox
vcflib
Version: 1.0.0_rc1
Conda Channel: bioconda
Summary:
Command-line tools for manipulating VCF files
vcftools
Version: 0.1.14
Conda Channel: bioconda
Summary:
A set of tools written in Perl and C++ for working with VCF files.