tnseq-transit
statistical calculations of essentiality of genes or genomic regions
Command lineScience
Not tested on a device yet. What that means
Commands in the package
transittransit-tpp
About tnseq-transit
From Debian's package description
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.
From Debian's description of the tnseq-transit package, under that package's license.
Dependencies
Depends on
Related apps
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- gnuastroGNU Astronomy Utilities programsCommand line
- gffreadGFF/GTF format conversions, region filtering, FASTA sequence extractionCommand line
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- fml-asmtool for assembling Illumina short reads in small regionsCommand line
R CommanderGraphical interface to the R environment for statistical computing
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the tnseq-transit package, under that package's license.
- Description: Debian's description of the tnseq-transit package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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