Paketti: trinityrnaseq (2.15.1+dfsg-5 ja muut)

[ Source: trinityrnaseq  ]

RNA-Seq De novo Assembly

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

Muut pakettiin trinityrnaseq liittyvät paketit

• dep: berkeley-express

  Streaming quantification for high-throughput sequencing

• dep: bowtie

  Ultrafast memory-efficient short read aligner

• dep: bowtie2

  ultrafast memory-efficient short read aligner

• dep: default-jre-headless

  Standard Java or Java compatible Runtime (headless)

• dep: jaligner

  Smith-Waterman algorithm with Gotoh's improvement

• dep: jellyfish

  count k-mers in DNA sequences

• dep: kallisto

  near-optimal RNA-Seq quantification

• dep: libc6 (>= 2.34) [ei alpha, ia64, sh4]

  GNU-C-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa libc6-udeb

  dep: libc6 (>= 2.37) [sh4]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU-C-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa libc6.1-udeb

  dep: libc6.1 (>= 2.37) [ia64]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, ppc64, ppc64el, x32]

  GCC:n apukirjasto

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sh4, sparc64]

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC:n apukirjasto

• dep: libgetopt-java

  GNU getopt - Java port

• dep: libgomp1 (>= 6)

  GCC OpenMP (GOMP) support library

• dep: libhts3 (>= 1.17) [ei amd64, arm64, ppc64el, riscv64]

  C library for high-throughput sequencing data formats

• dep: libhts3t64 (>= 1.17) [amd64, arm64, ppc64el, riscv64]

  C library for high-throughput sequencing data formats

• dep: libjung-free-java

  Java Universal Network/Graph Framework

• dep: libstdc++6 (>= 13.1)

  GNU standardi C++ -kirjasto, versio 3

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: liburi-perl

  module to manipulate and access URI strings

• dep: libwww-perl

  simple and consistent interface to the world-wide web

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: parafly

  parallel command processing using OpenMP

• dep: perl

  Larry Wallin kieli tekstitiedostojen analysointia ja raportointia varten

• dep: python3

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

• dep: python3-htseq

  Python3 high-throughput genome sequencing read analysis utilities

• dep: r-base-core

  GNU R core of statistical computation and graphics system

• dep: rsem

  RNA-Seq by Expectation-Maximization

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: subread

  toolkit for processing next-gen sequencing data

• dep: trimmomatic

  flexible read trimming tool for Illumina NGS data

• dep: zlib1g (>= 1:1.1.4)

  pakkauskirjaston ajonaikaistiedostot

• rec: curl

  command line tool for transferring data with URL syntax

• rec: gmap

  spliced and SNP-tolerant alignment for mRNA and short reads

• rec: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• rec: picard-tools

  Command line tools to manipulate SAM and BAM files

• rec: python3-hisat2

  Python scripts accompanying hisat2

• rec: python3-numpy

  Fast array facility to the Python language (Python 3)

• rec: r-bioc-biobase

  base functions for Bioconductor

• rec: r-bioc-ctc

  Cluster and Tree Conversion

• rec: r-bioc-deseq2

  R package for RNA-Seq Differential Expression Analysis

• rec: r-bioc-dexseq

  GNU R inference of differential exon usage in RNA-Seq

• rec: r-bioc-edger

  Empirical analysis of digital gene expression data in R

• rec: r-bioc-goseq

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

• rec: r-bioc-qvalue

  GNU R package for Q-value estimation for FDR control

• rec: r-bioc-rots

  GNU R Teproducibility-Optimized Test Statistic

• rec: r-cran-ape

  GNU R package for Analyses of Phylogenetics and Evolution

• rec: r-cran-argparse

  GNU R command line parser for optional and positional arguments

• 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-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-cran-kernsmooth

  GNU R package for kernel smoothing and density estimation

• rec: r-cran-readr

  GNU R package to read rectangular text data

• rec: r-cran-tidyverse

  Easily Install and Load the 'Tidyverse'

• rec: rna-star

  ultrafast universal RNA-seq aligner

• rec: salmon

  wicked-fast transcript quantification from RNA-seq data

• rec: tabix

  generic indexer for TAB-delimited genome position files

• rec: trinityrnaseq-examples

  RNA-Seq De novo Assembly common example and testing files

• sug: collectl

  Utility to collect Linux performance data

• sug: r-bioc-tximport

  transcript-level estimates for biological sequencing

• sug: r-bioc-tximportdata

  GNU R various transcript abundance quantifiers

• sug: transdecoder

  find coding regions within RNA transcript sequences

Imuroi trinityrnaseq

Imurointi kaikille saataville arkkitehtuureille

Arkkitehtuuri	Versio	Paketin koko	Koko asennettuna	Tiedostot
alpha (epävirallinen siirros)	2.15.1+dfsg-2	1,656.3 kt	8,135.0 kt	[tiedostoluettelo]
amd64	2.15.1+dfsg-5+b1	1,679.8 kt	7,456.0 kt	[tiedostoluettelo]
arm64	2.15.1+dfsg-5+b1	1,616.8 kt	7,740.0 kt	[tiedostoluettelo]
ia64 (epävirallinen siirros)	2.15.1+dfsg-2	1,717.4 kt	9,611.0 kt	[tiedostoluettelo]
m68k (epävirallinen siirros)	2.15.1+dfsg-2	1,654.5 kt	7,399.0 kt	[tiedostoluettelo]
ppc64 (epävirallinen siirros)	2.15.1+dfsg-2	1,664.4 kt	8,572.0 kt	[tiedostoluettelo]
ppc64el	2.15.1+dfsg-5+b1	1,667.4 kt	8,316.0 kt	[tiedostoluettelo]
riscv64	2.15.1+dfsg-5+b1	1,660.8 kt	6,824.0 kt	[tiedostoluettelo]
sh4 (epävirallinen siirros)	2.15.1+dfsg-2	1,726.5 kt	7,736.0 kt	[tiedostoluettelo]
sparc64 (epävirallinen siirros)	2.15.1+dfsg-2	1,576.3 kt	18,081.0 kt	[tiedostoluettelo]
x32 (epävirallinen siirros)	2.15.1+dfsg-2	1,676.7 kt	7,287.0 kt	[tiedostoluettelo]