trxtools

version 0.3.0

trxtools is set of bioinformatic tools and methods to facilitate analysis of transcriptional data.

Major focus is put on postprocessing of high-troughput sequencing data originating from the followin methods:

• CRAC/CLIP

• RNA-seq

• tRNA-seq

• NET-seq

• ChIP-seq

Some functions in the package use a specific file naming system:

'expID', 'expDate', 'protein', 'condition1', 'condition2', 'condition3'

i.e. C123_JK050420_POLR2A-FLAG_wt_arsenite30min will be used for an experiment C123 conducted by a person JK on 020420. This is puldown with POLR2A-FLAG in wt cells after arsenite30min

Reporting bugs

If you encounter a bug, please report it on the GitHub issue tracker.

Contents

• Scripts
  • Main scripts
    • SAM2profilesGenomic.py
    • SAM2profilesTranscripts.py
    • genomeNascentFolding.py
  • Supporting scripts
    • genome2WindowsGTF.py
    • csv2pickle.py
    • mergeSalmon.py
    • fasta2slidingWindows.py
    • polyAfraction.py

• trxtools package
  • trxtools.sam module
    • trxtools.sam.SAMgeneral submodule
    • trxtools.sam.SAMgenome submodule
    • trxtools.sam.SAMtranscripts submodule
  • trxtools.BigWig module
  • trxtools.metaprofiles module
  • trxtools.assays module
  • trxtools.go_enrichment module
  • trxtools.methods module
  • trxtools.nascent module
  • trxtools.plotting module
  • trxtools.profiles module
  • trxtools.secondary module

• Release information
  • Reporting bugs
  • Versions
    • v0.3.0
    • v0.2.2
    • v0.2.1
  • Authors

Indices and tables

• Index

• Module Index