Paket: trinityrnaseq (2.15.1+dfsg-2) [debports]

[ Quellcode:  ]

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.

Andere Pakete mit Bezug zu trinityrnaseq

• dep: berkeley-express

  Streaming quantification for high-throughput sequencing

• dep: bowtie

  Ultraschnelles und speichersparendes Alignmentprogramm für kurze DNA-Sequenzen

• dep: bowtie2

  Ultraschnelles und speichersparendes Alignmentprogramm für kurze DNA-Sequenzen

• dep: default-jre-headless

  Standard Java or Java compatible Runtime (headless)

• dep: jaligner

  Smith-Waterman algorithm with Gotoh's improvement

• dep: jellyfish

  Zählt k-mere in DNA-Sequenzen

• dep: kallisto

  near-optimal RNA-Seq quantification

• dep: libc6.1 (>= 2.37)

  GNU-C-Bibliothek: Laufzeitbibliotheken
  auch ein virtuelles Paket, bereitgestellt durch libc6.1-udeb

• dep: libgcc-s1 (>= 4.2)

  GCC Support-Bibliothek

• dep: libgetopt-java

  GNU getopt - Java-Portierung

• dep: libgomp1 (>= 6)

  Unterstützungsbibliothek für GCC OpenMP (GOMP)

• dep: libhts3 (>= 1.17)

  C-Bibliothek für Hochdurchsatz-Sequenzierungsdatenformate

• dep: libjung-free-java

  Java Universal Network/Graph Framework

• dep: libstdc++6 (>= 13.1)

  GNU-Implementierung der Standard-C++-Bibliothek (Version 3)

• dep: libunwind8

  Bibliothek zur Ermittlung der Aufrufkette eines Programms - Laufzeit

• dep: liburi-perl

  Modul für Zugriff auf und Manipulation von URI-Zeichenketten

• dep: libwww-perl

  Einfache und konsistente Schnittstelle zum World Wide Web

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: parafly

  parallel command processing using OpenMP

• dep: perl

  Larry Wall's Practical Extraction und Report Language

• 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 - System für statistische Berechnungen und Grafik - Kern

• 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)

  Kompressions-Bibliothek - Laufzeit

• rec: curl

  Befehlszeilenwerkzeug zur Dateiübertragung mit 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

  Empirische Analyse von digitalen Genexpressionsdaten mit R

• rec: r-bioc-goseq

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

• rec: r-bioc-qvalue

  »GNU R«-Paket zur Q-Wert-Bestimmung für FDR-Steuerung

• 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-Paket zur Cluster-Analyse von 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-Paket für Kernel-Regression und Dichteschätzung

• 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

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