trinityrnaseq

dep: [libc6] (>= 2.38)

GNU C Library: Shared libraries

dep: [libgcc-s1] (>= 3.0)

GCC support library

dep: [libgomp1] (>= 6)

GCC OpenMP (GOMP) support library

dep: [libhts3t64] (>= 1.17)

C library for high-throughput sequencing data formats

dep: [libstdc++6] (>= 14)

GNU Standard C++ Library v3

dep: [zlib1g] (>= 1:1.1.4)

compression library - runtime

dep: [perl] [any]

Larry Wall's Practical Extraction and Report Language

dep: [jaligner]

Smith-Waterman algorithm with Gotoh's improvement

dep: [libgetopt-java]

GNU getopt - Java port

dep: [libjung-free-java]

Java Universal Network/Graph Framework

dep: [bowtie]

Ultrafast memory-efficient short read aligner

dep: [bowtie2]

ultrafast memory-efficient short read aligner

dep: [libwww-perl]

simple and consistent interface to the world-wide web

dep: [default-jre-headless]

Standard Java or Java compatible Runtime (headless)

dep: [samtools]

processing sequence alignments in SAM, BAM and CRAM formats

dep: [jellyfish]

count k-mers in DNA sequences

dep: [r-base-core]

GNU R core of statistical computation and graphics system

dep: [rsem]

RNA-Seq by Expectation-Maximization

dep: [berkeley-express]

Streaming quantification for high-throughput sequencing

dep: [trimmomatic]

flexible read trimming tool for Illumina NGS data

dep: [parafly]

parallel command processing using OpenMP

dep: [ncbi-blast+]

next generation suite of BLAST sequence search tools

dep: [python3]

interactive high-level object-oriented language (default python3 version)

dep: [liburi-perl]

module to manipulate and access URI strings

dep: [python3-htseq]

Python3 high-throughput genome sequencing read analysis utilities

dep: [subread]

toolkit for processing next-gen sequencing data

dep: [kallisto]

near-optimal RNA-Seq quantification

rec: [curl]

command line tool for transferring data with URL syntax

rec: [trinityrnaseq-examples]

RNA-Seq De novo Assembly common example and testing files

rec: [picard-tools]

Command line tools to manipulate SAM and BAM files

rec: [tabix]

generic indexer for TAB-delimited genome position files

rec: [gmap]

spliced and SNP-tolerant alignment for mRNA and short reads

rec: [salmon]

wicked-fast transcript quantification from RNA-seq data

rec: [rna-star]

ultrafast universal RNA-seq aligner

rec: [hisat2]

graph-based alignment of short nucleotide reads to many genomes

rec: [r-cran-tidyverse]

Easily Install and Load the 'Tidyverse'

rec: [r-cran-readr]

GNU R package to read rectangular text data

rec: [r-bioc-edger]

Empirical analysis of digital gene expression data in R

rec: [r-bioc-deseq2]

R package for RNA-Seq Differential Expression Analysis

rec: [r-bioc-rots]

GNU R Teproducibility-Optimized Test Statistic

rec: [r-cran-cluster]

GNU R package for cluster analysis by Rousseeuw et al

rec: [r-cran-fastcluster]

Fast hierarchical clustering routines for GNU R

rec: [r-bioc-ctc]

Cluster and Tree Conversion

rec: [r-bioc-goseq]

GNU R gene ontology analyser for RNA-seq and other length biased data

rec: [r-cran-goplot]

GNU R visualization of functional analysis data

rec: [r-cran-gplots]

GNU R package with tools for plotting data by Greg Warnes et al

rec: [r-bioc-dexseq]

GNU R inference of differential exon usage in RNA-Seq

rec: [r-cran-ape]

GNU R package for Analyses of Phylogenetics and Evolution

rec: [r-bioc-biobase]

base functions for Bioconductor

rec: [r-bioc-qvalue]

GNU R package for Q-value estimation for FDR control

rec: [r-cran-argparse]

GNU R command line parser for optional and positional arguments

rec: [r-cran-kernsmooth]

GNU R package for kernel smoothing and density estimation

rec: [python3-numpy]

Python library for numerical computations (Python 3)

rec: [python3-hisat2]

Python scripts accompanying hisat2

sug: [collectl]

Utility to collect Linux performance data

sug: [transdecoder]

find coding regions within RNA transcript sequences

sug: [r-bioc-tximport]

transcript-level estimates for biological sequencing

sug: [r-bioc-tximportdata]

GNU R various transcript abundance quantifiers