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

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.

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