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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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Versioning


No version available

Maintainers


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

Publication for rDiff

rDiff citations

 (28)
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

[…] eins/splicing 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, the r […]

call_split

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
call_split See protocol

[…] 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 were […]

library_books

Understanding the anticorrosive protective mechanisms of modified epoxy coatings with improved barrier, active and self healing functionalities: EIS and spectroscopic techniques

2017
Sci Rep
PMCID: 5688088
PMID: 29142312
DOI: 10.1038/s41598-017-15845-0

[…] burg finite diffusion impedance element), while the equivalent circuit in Fig.  exhibited three-time constants – the third constant composed of diffusion capacitive component (CPEdff) and resistance (Rdiff). Meanwhile, the Warburg impedance (ZW) in the second circuit (Fig. ) represents the diffusion of corrosive ions within the coating pores,. The electrical circuit in Fig.  was adopted to mostly […]

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

[…] significance 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, and whether […]

library_books

Sample entropy reveals an age related reduction in the complexity of dynamic brain

2017
Sci Rep
PMCID: 5554148
PMID: 28801672
DOI: 10.1038/s41598-017-08565-y

[…] ion coefficients to investigate these associations between SampEn and age, conditioning on gender, education, and head motion. For each functional connection, using the webpage http://vassarstats.net/rdiff.html, we calculated a value of Z that could be applied to assess the significance of the difference between the partial correlation coefficient of the healthy group and that of the patient group […]

call_split

Relationships of work characteristics to job satisfaction, turnover intention, and burnout among doctors in the district public private mixed health system of Bangladesh

2017
PMCID: 5480190
PMID: 28637454
DOI: 10.1186/s12913-017-2369-y
call_split See protocol

[…] he outcomes of interest. Ninty 5 % bias corrected and accelerated bootstrap confidence intervals (BCa CIs) were used to assess significance of correlation. An online programme (http://vassarstats.net/rdiff.html) was used to test any significant differences in the corresponding correlation coefficients between the public and private sector using Fisher’s r-to-z-transformation. A p-value <.05 was re […]

Citations

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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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