Paketti: tnseq-transit (3.3.4-1) [debports]

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statistical calculations of essentiality of genes or genomic regions

This is a software that can be used to analyze Tn-Seq datasets. It includes various statistical calculations of essentiality of genes or genomic regions (including conditional essentiality between 2 conditions). These methods were developed and tested as a collaboration between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M)

TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1 or Tn5 datasets.

TRANSIT assumes you have already done pre-processing of raw sequencing files (.fastq) and extracted read counts into a .wig formatted file. The .wig file should contain the counts at all sites where an insertion could take place (including sites with no reads). For Himar1 datasets this is all TA sites in the genome. For Tn5 datasets this would be all nucleotides in the genome.

Muut pakettiin tnseq-transit liittyvät paketit

• dep: bwa

  Burrows-Wheeler Aligner

• dep: python3

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

• dep: python3-matplotlib

  Python based plotting system in a style similar to Matlab

• dep: python3-numpy

  Fast array facility to the Python language (Python 3)

• dep: python3-pil

  Python Imaging Library (Python3)

• dep: python3-pkg-resources

  Package Discovery and Resource Access using pkg_resources

• dep: python3-pubsub

  Python 3 publish-subcribe library

• dep: python3-scipy

  scientific tools for Python 3

• dep: python3-sklearn

  Python modules for machine learning and data mining - Python 3

• dep: python3-statsmodels

  Python3 module for the estimation of statistical models

• dep: python3-wxgtk4.0

  Python 3 interface to the wxWidgets Cross-platform C++ GUI toolkit

Imuroi tnseq-transit

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