Paket: rsem (1.3.3+dfsg-3 ve diğerleri)

[ Kaynak: rsem  ]

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.

rsem ile İlgili Diğer Paketler

• dep: bowtie

  Ultrafast memory-efficient short read aligner

  ya da bowtie2

  ultrafast memory-efficient short read aligner

• dep: libc6 (>= 2.15) [m68k]

  GNU C Library: Shared libraries
  ayrıca şunun tarafından sağlanan bir sanal paket libc6-udeb

  dep: libc6 (>= 2.29) [sh4]

  dep: libc6 (>= 2.34) [alpha, m68k, sh4 değil]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU C Library: Shared libraries
  ayrıca şunun tarafından sağlanan bir sanal paket libc6.1-udeb

• dep: libgcc-s1 (>= 3.0) [alpha, hppa, m68k, riscv64, sh4, sparc64 değil]

  GCC support library

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

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: libgcc1 (>= 1:4.2) [sh4]

  Paket mevcut değil

• dep: libgcc2 (>= 4.2.1) [m68k]

  Paket mevcut değil

• dep: libhts3 (>= 1.10) [sh4]

  C library for high-throughput sequencing data formats

• dep: libhts3t64 (>= 1.17) [m68k, sh4 değil]

  C library for high-throughput sequencing data formats

• dep: libstdc++6 (>= 13.1) [m68k, sh4 değil]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 5.2) [m68k]

  dep: libstdc++6 (>= 9) [sh4]

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• dep: python [m68k]

  Paket mevcut değil

• dep: python3 [m68k değil]

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

• dep: r-base-core

  GNU R core of statistical computation and graphics system

• dep: zlib1g (>= 1:1.1.4) [sh4, sparc64]

  compression library - runtime

  dep: zlib1g (>= 1:1.2.3.3) [m68k]

• sug: hisat2 [m68k, sh4 değil]

  graph-based alignment of short nucleotide reads to many genomes

• sug: r-bioc-ebseq

  R package for RNA-Seq Differential Expression Analysis

rsem indir

Tüm mevcut mimariler için indir

Mimari	Sürüm	Paket Boyutu	Kurulu Boyut	Dosyalar
alpha (resmi olmayan port)	1.3.3+dfsg-3+b1	35.275,3 kB	37.674,0 kB	[dosya listesi]
amd64	1.3.3+dfsg-3+b1	35.295,5 kB	37.100,0 kB	[dosya listesi]
arm64	1.3.3+dfsg-3+b1	35.231,6 kB	37.212,0 kB	[dosya listesi]
hppa (resmi olmayan port)	1.3.3+dfsg-3+b1	35.265,2 kB	36.898,0 kB	[dosya listesi]
m68k (resmi olmayan port)	1.2.26+dfsg-2	402,7 kB	2.457,0 kB	[dosya listesi]
mips64el	1.3.3+dfsg-3+b1	35.248,4 kB	37.606,0 kB	[dosya listesi]
ppc64 (resmi olmayan port)	1.3.3+dfsg-3+b1	35.258,0 kB	37.532,0 kB	[dosya listesi]
ppc64el	1.3.3+dfsg-3+b1	35.270,7 kB	37.532,0 kB	[dosya listesi]
riscv64	1.3.3+dfsg-3+b2	35.274,5 kB	36.648,0 kB	[dosya listesi]
s390x	1.3.3+dfsg-3+b1	35.294,8 kB	37.180,0 kB	[dosya listesi]
sh4 (resmi olmayan port)	1.3.2+dfsg-2+b1	35.337,5 kB	36.915,0 kB	[dosya listesi]
sparc64 (resmi olmayan port)	1.3.3+dfsg-3+b1	35.221,8 kB	50.502,0 kB	[dosya listesi]
x32 (resmi olmayan port)	1.3.3+dfsg-3+b1	35.299,9 kB	37.017,0 kB	[dosya listesi]