Package: stringtie (2.2.1+ds-3 and others)

[ Source: stringtie  ]

assemble short RNAseq reads to transcripts

The abundance of transcripts in a human tissue sample can be determined by RNA sequencing. The exact sequence sampled may be random, depending on the technology used. And it may be short, i.e. shorter than the transcript. At some point, many shorter reads need to be assembled to the model the complete transcripts.

StringTie knows how to assemble of RNA-Seq into potential transcripts without the need of a reference genome and provides a quantification also of the splice variants.

Other Packages Related to stringtie

• dep: libbz2-1.0 [sparc64]

  high-quality block-sorting file compressor library - runtime

• dep: libc6 (>= 2.34) [not alpha, arm64, ia64, sh4]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.37) [sh4]

  dep: libc6 (>= 2.38) [arm64]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

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

• dep: libgcc-s1 (>= 3.4) [alpha, amd64, i386, mips64el, ppc64, riscv64, sh4, x32]

  GCC support library

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

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

  dep: libgcc-s1 (>= 4.3) [sparc64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support library

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: libhts3t64 (>= 1.17)

  C library for high-throughput sequencing data formats

• dep: libstdc++6 (>= 4.1.1)

  GNU Standard C++ Library v3

• dep: python3

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

• dep: zlib1g (>= 1:1.1.4) [sparc64]

  compression library - runtime

• rec: stringtie-examples

  Package not available

• sug: cufflinks

  Transcript assembly, differential expression and regulation for RNA-Seq

Download stringtie

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.2.1+ds-3+b1	377.7 kB	1,263.0 kB	[list of files]
amd64	2.2.1+ds-3+b1	404.4 kB	1,025.0 kB	[list of files]
arm64	2.2.1+ds-3+b2	363.9 kB	1,005.0 kB	[list of files]
armel	2.2.1+ds-3+b1	342.6 kB	972.0 kB	[list of files]
armhf	2.2.1+ds-3+b1	349.7 kB	684.0 kB	[list of files]
hppa (unofficial port)	2.2.1+ds-3+b1	347.3 kB	1,124.0 kB	[list of files]
i386	2.2.1+ds-3+b1	433.3 kB	1,284.0 kB	[list of files]
ia64 (unofficial port)	2.2.1+ds-3+b1	504.8 kB	2,359.0 kB	[list of files]
m68k (unofficial port)	2.2.1+ds-3+b1	334.4 kB	932.0 kB	[list of files]
mips64el	2.2.1+ds-3+b1	357.5 kB	1,239.0 kB	[list of files]
ppc64 (unofficial port)	2.2.1+ds-3+b1	410.1 kB	1,325.0 kB	[list of files]
ppc64el	2.2.1+ds-3+b1	414.9 kB	1,261.0 kB	[list of files]
riscv64	2.2.1+ds-3+b1	390.0 kB	773.0 kB	[list of files]
s390x	2.2.1+ds-3+b1	418.4 kB	1,121.0 kB	[list of files]
sh4 (unofficial port)	2.2.1+ds-3+b1	464.2 kB	877.0 kB	[list of files]
sparc64 (unofficial port)	2.2.1+ds-3+b1	351.1 kB	1,073.0 kB	[list of files]
x32 (unofficial port)	2.2.1+ds-3+b1	401.5 kB	1,004.0 kB	[list of files]