gencore_rnaseq_malaria
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-cummerbund
Version: 2.12.1
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: 1.10.1
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-deseq
Version: 1.22.1
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.
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
Version: 2.2.1
Conda Channel: bioconda
Summary:
Transcriptome assembly and differential expression analysis for RNA-Seq.
gatk
Version: 3.5
Conda Channel: bioconda
Summary:
The full Genome Analysis Toolkit (GATK) framework, license restricted.
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: 2.0.1
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
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.
tophat
Version: 2.1.0
Conda Channel: bioconda
Summary:
A spliced read mapper for RNA-Seq
trimmomatic
Version: 0.35
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.