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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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Maintainers


  • person_outline Gunnar Rätsch
  • person_outline Gunnar Rätsch
  • person_outline Philipp Drewe

Publication for rDiff

rDiff citations

 (46)
library_books

Observation of negative differential resistance in mesoscopic graphene oxide devices

2018
Sci Rep
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). […]

library_books

A Genomic View of Alternative Splicing of Long Non coding RNAs during Rice Seed Development Reveals Extensive Splicing and lncRNA Gene Families

2018
Front Plant Sci
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, […]

library_books

Metacognitive Aspects of Executive Function Are Highly Associated with Social Functioning on Parent Rated Measures in Children with Autism Spectrum Disorder

2018
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 […]

library_books

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder Enriched Interactions

2017
Int J Mol Sci
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 […]

library_books

Assessing the Role of Inhibition in Stabilizing Neocortical Networks Requires Large Scale Perturbation of the Inhibitory Population

2017
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 […]

library_books

Post traumatic stress disorder moderates the relationship between trauma exposure and chronic pain

2017
PMCID: 5632777
PMID: 29038680
DOI: 10.1080/20008198.2017.1375337

[…] of the difference in trauma exposure and pain correlations in the ptsd and the no ptsd groups (r = .26 and .03, respectively) (performed with an online calculator: http://vassarstats.net/rdiff.html) showed that these two correlations were not statistically significantly different (z = −0.82, p = 0.4122).figure 1. , our fifth analysis investigated the pain treatment outcome, […]


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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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