Allim specifications

Information


Unique identifier OMICS_05504
Name Allim
Alternative name ALLelic Imbalance Metre
Software type Application/Script, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
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.
Input format FASTQ+FASTQ+FASTA,FASTA+FASTA,FASTQ,GTF
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.
Operating system Unix/Linux, Mac OS
Programming languages Python, R
License Mozilla Public License version 2.0
Computer skills Advanced
Version 1.2
Stability Stable
Requirements Biopython, PICARD, SAMTOOLS, BedTools, GSNAP, NumPy, RPy, car, multcomp, edgeR, limma
Maintained Yes

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Documentation


Maintainer


  • person_outline Christian Schlotterer <>

Additional information


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

Allim article

Allim 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
Allim funding source(s)
Supported by the Austrian Science Funds (FWF) grant P22834 and by the Volkswagen Foundation.

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