Allim specifications

Unique identifier:
OMICS_05504
Software type:
Application/Script, Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTQ+FASTQ+FASTA,FASTA+FASTA,FASTQ,GTF
Operating system:
Unix/Linux, Mac OS
License:
Mozilla Public License version 2.0
Version:
1.2
Requirements:
Biopython, PICARD, SAMTOOLS, BedTools, GSNAP, NumPy, RPy, car, multcomp, edgeR, limma
Name:
ALLelic Imbalance Metre
Interface:
Command line interface
Input data:
A file for each parent RNA-Seq data or a file for each parent genomic DNA sequencing data and a file containing the reference genome; or a file for each parent genome; or a file including hybrid RNA-Seq; or a file with reference gene annotation.
Output data:
Some expression tables for allele specific expression on the gene and the exon level or an allelic imbalance test with FDR corrected p-values.
Programming languages:
Python, R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

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Allim distribution

download

Allim support

Documentation

Maintainer

  • Christian Schlotterer <>

Additional information

https://code.google.com/archive/p/allim/

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Publications

Institution(s)

Institut fur Populationsgenetik, Vetmeduni Vienna, Vienna, Austria; Institut fur Evolution und Biodiversitat, Universitat Munster, Munster, Germany; Institut fur Statistik, University of Vienna, Vienna, Austria

Funding source(s)

Supported by the Austrian Science Funds (FWF) grant P22834 and by the Volkswagen Foundation.

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