Package: cufflinks (2.2.1+dfsg.1-9) [non-free]

[ Source: cufflinks  ]

Transcript assembly, differential expression and regulation for RNA-Seq

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

This package provides the binary of cufflinks and associated tools, i.e. compress_gtf, cuffcompare, cuffdiff, cuffmerge, cuffnorm, cuffquant and gtf_to_sam.

Tags: Biology: Nucleic Acids, Field: Biology, field::biology:bioinformatics, implemented-in::c++, Role: Program, Works with: Biological Sequence

Other Packages Related to cufflinks

• dep: libboost-serialization1.74.0 (>= 1.74.0)

  serialization library for C++

• dep: libboost-thread1.74.0 (>= 1.74.0)

  portable C++ multi-threading

• dep: libc6 (>= 2.29)

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

• dep: libgcc-s1 (>= 4.1)

  GCC support library

• dep: libstdc++6 (>= 11)

  GNU Standard C++ Library v3

• dep: python3

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

• dep: zlib1g (>= 1:1.2.3.3)

  compression library - runtime

• rec: gffread

  GFF/GTF format conversions, region filtering, FASTA sequence extraction

• enh: tophat

  Package not available

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