Paket: rsem (1.3.3+dfsg-3 und andere) [debports]

[ Quellcode:  ]

RNA-Seq by Expectation-Maximization

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute’s Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator.

Andere Pakete mit Bezug zu rsem

• dep: bowtie

  Ultraschnelles und speichersparendes Alignmentprogramm für kurze DNA-Sequenzen

  oder bowtie2

  Ultraschnelles und speichersparendes Alignmentprogramm für kurze DNA-Sequenzen

• dep: libc6 (>= 2.34)

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

• dep: libgcc-s1 (>= 3.4)

  GCC Support-Bibliothek

• dep: libhts3t64 (>= 1.17)

  C-Bibliothek für Hochdurchsatz-Sequenzierungsdatenformate

• dep: libstdc++6 (>= 13.1)

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

• dep: perl

  Larry Wall's Practical Extraction und Report Language

• dep: python3

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

• dep: r-base-core

  GNU R - System für statistische Berechnungen und Grafik - Kern

• dep: zlib1g (>= 1:1.1.4)

  Kompressions-Bibliothek - Laufzeit

• sug: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• sug: r-bioc-ebseq

  R package for RNA-Seq Differential Expression Analysis

rsem herunterladen

Download für alle verfügbaren Architekturen

Architektur	Version	Paketgröße	Größe (installiert)	Dateien
sparc64 (inoffizielle Portierung)	1.3.3+dfsg-3+b1	35.221,8 kB	50.502,0 kB	[Liste der Dateien]