VARiD protocols

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VARiD specifications

Information


Unique identifier OMICS_02163
Name VARiD
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data The alignments and the reference files.
Input format SAM,FASTA
Biological technology Life Technologies
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.7f
Stability Stable
Source code URL http://compbio.cs.utoronto.ca/varid/releases/varid-1.0.7f.tar.gz
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Adrian V. Dalca <>

Additional information


http://compbio.cs.utoronto.ca/varid/releases/README

Publication for VARiD

VARiD in pipeline

2012
PMCID: 3531709
PMID: 23293637
DOI: 10.3389/fimmu.2012.00386

[…] (pandey et al., ) identifies indels that appear only in hpts near the primers and discards them. the program does not identify indels occurring far from the primers. varscan (koboldt et al., ) and varid (dalca et al., ) can identify indels, but these programs deal with variability and single nucleotide polymorphism (snp) identification, and do not distinguish between legitimate and artifact […]


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VARiD in publications

 (7)
PMCID: 5902285
PMID: 29620634
DOI: 10.1097/MD.0000000000010231

[…] of the lbw and bsa on the validity of the contrast agent volume on ctv and ctpa protocols., we hypothesised that the bw-tailored protocol would be suitable to keep the contrast agent volume to yield varid venous enhancement on ctv images. the purpose of this study was to evaluate the relationship between the required contrast agent dose to acquire diagnostic-quality ctv with a bw-tailored […]

PMCID: 5867455
PMID: 29599826
DOI: 10.3892/etm.2018.5788

[…] china) for providing help with data analysis., the authors declare that they have no competing interests., screening of 1,166 peaks corresponding to the number of substances in the serum after varid was used to import the software., model group vs. control group. rt, retention time of the substance; koa, knee osteoarthritis; vip, variable importance […]

PMCID: 5646968
PMID: 29067456
DOI: 10.3892/mmr.2017.7078

[…] control group; up, relatively high in the sgjpf group vs. model group; down, relatively low in the sgjpf group vs. model group., p<0.01, p<0.05 vs. control group, p<0.05 vs. model group. varid, serum screening of 469 peaks to the serial number of compound; rt, retention time of substance; vip, variable importance projection; sgjpf, shu gan jian pi […]

PMCID: 5525970
PMID: 28810615
DOI: 10.3892/etm.2017.4668

[…] shanghai, china) for providing help with data analysis., 519 peaks of the gc/ms spectra of the model and control groups were screened, corresponding to the number of the substance in serum when the varid was imported into the software, vip values >1.0 were selected as changed metabolites. from this, 7 metabolites from serum were demonstrated to be significantly altered., p<0.01, p<0.05 […]

PMCID: 4775768
PMID: 26989506
DOI: 10.1155/2016/5690935

[…] index on day 30 after intragastric administration of xfc. data represent the mean ± sd (n = 8). ∗∗ p < 0.01 compared with healthy group; ## p < 0.01 compared with untreated group., note: varid represents urine screening 1166 peak to the serial number of compound; rt represents retention time of compound. a variable importance in the projection (vip) was obtained from opls-da model […]


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VARiD institution(s)
Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Department of Computer Science, Stanford University, Stanford, CA, USA; Scripps Genomic Medicine, The Scripps Research Institute, La Jolla, CA, USA; Donnelly Centre and the Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
VARiD funding source(s)
Supported by National Sciences and Engineering Research Council (NSERC) of Canada; Mathematics of Information Technology and Complex Systems (MITACS) grant; and Life Technologies (Applied Biosystems).

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