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rDiff specifications

Information


Unique identifier OMICS_01338
Name rDiff
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BAM+GFF3
Output format TAB+MAT
Biological technology Illumina, Pacific Biosciences
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
Octave or Matlab, Scipy, Samtools, wget
Maintained Yes

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  • person_outline Gunnar Rätsch <>
  • person_outline Gunnar Rätsch <>
  • person_outline Philipp Drewe <>

Publication for rDiff

rDiff in pipeline

2014
PMCID: 4492470
PMID: 25079319
DOI: 10.1038/nature13485

[…] annotation. then the bed file and footprint bam files were given as an input to samtools to generate new bam files only included exonic alignment. we input the exonic bam files of two conditions to rdiff to identify genes that presented significant change in ribosomal distribution. in detail, we performed a nonparametric test implemented in rdiff to detect differential read densities. rdiff […]

rDiff in publications

 (46)
PMCID: 5940784
PMID: 29739956
DOI: 10.1038/s41598-018-22355-0

[…] \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${r}_{diff}=\frac{{\rm{\delta }}v}{{\rm{\delta }}i} < 0$$\end{document}rdiff=δvδi<0) (fig. ); this ndr peak maintained its repeatability even after 14 subsequent sweeps (see supplementary information, section f, for further voltage sweep across the go device). […]

PMCID: 5808331
PMID: 29467783
DOI: 10.3389/fpls.2018.00115

[…] factors. to elucidate the potential importance of alternative splicing in seed development, we chose to analyze rna-seq datasets with rmats. a comprehensive analysis of several methods (rdiff, diffsplice, rmats, cuffdiff, and desseq) designed to identify alternative splicing in rna-seq datasets identified almost no convergence in the overall predictions (liu et al., ). however, […]

PMCID: 5767603
PMID: 29375332
DOI: 10.3389/fnbeh.2017.00258

[…] used to investigate differences in the distribution of autism diagnoses and comorbid adhd. the differences between the subgroups correlation coefficients were calculated using http://vassarstats.net/rdiff.html (two-tailed). because of small subgroup sizes and no significant differences between the correlation coefficients, the regression analyses were done on the total sample and sex and age […]

PMCID: 5751360
PMID: 29257115
DOI: 10.3390/ijms18122761

[…] from a given set. we represented each set of ten measurements with a mean value and we quantified the magnitude of the difference between the two sets of proteins by the relative difference (rdiff) between the two corresponding means defined as:(2)rdiff=meandisorder enriched hub ppis−meanremaining hub ppismin{meandisorder enriched hub ppis, meanremaining hub ppis}×100%, positive rdiff […]

PMCID: 5719979
PMID: 29074575
DOI: 10.1523/JNEUROSCI.0963-17.2017

[…] the normal state (rbase) and during perturbation (rpert) were computed by averaging over time, trials, and the subpopulation. the change in the firing rate due to perturbation was then computed as rdiff = rpert − rbase. because the perturbation is performed by decreasing the input to a fraction of inhibitory subpopulation, a positive rdiff for the perturbed inhibitory fraction implies […]

rDiff institution(s)
Computational Biology Center, Sloan-Kettering Institute, New York, NY, USA; Friedrich Miescher Laboratory of the Max-Planck Society, Tubingen, Germany; Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems, Tubingen, Germany; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany; Center for Plant Mol. Biology, University of Tubingen, Tubingen, Germany; Center for Bioinformatics, University of Tubingen, Tubingen, Germany
rDiff funding source(s)
Supported by Volkswagen foundation and Marie Curie FP7 fellowship; German Research Foundation [WA2167/4-1; RA1894/1-1 and RA1894/2-1]; Emmy Noether fellowship [WA2167/2-1]. MSKCC Center for Translational Cancer Genomic Analysis [U24 CA143840]; and Sloan-Kettering Institute core funding.

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