CrispRVariants statistics

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Number of citations per year for the bioinformatics software tool CrispRVariants
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CrispRVariants specifications

Information


Unique identifier OMICS_12975
Name CrispRVariants
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data Set of sequences aligned to a reference genome
Input format BAM, AB1, FASTQ
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.8.0
Stability Stable
Requirements
AnnotationDbi, methods, grid, IRanges, GenomicRanges, Rsamtools, utils, testthat, GenomeInfoDb, Biostrings, rtracklayer, BiocStyle, grDevices, GenomicAlignments, R(>=3.5), BiocParallel, GenomicFeatures, rmarkdown, knitr, reshape2, VariantAnnotation, gridExtra, gdata, S4Vectors(>=0.9.38), ggplot2(>=2.2.0), sangerseqR
Maintained Yes

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Documentation


Maintainer


  • person_outline Helen Lindsay

Information


Unique identifier OMICS_12975
Name CrispRVariants
Interface Web user interface
Restrictions to use None
Input data Set of sequences aligned to a reference genome
Input format BAM, AB1, FASTQ
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Helen Lindsay

Publication for CrispRVariants

CrispRVariants citations

 (3)
library_books

A Rapid CRISPR/Cas based Mutagenesis Assay in Zebrafish for Identification of Genes Involved in Thyroid Morphogenesis and Function

2018
Sci Rep
PMCID: 5884836
PMID: 29618800
DOI: 10.1038/s41598-018-24036-4

[…] ll as deep-sequencing techniques,,. For our studies, we identified Illumina HiSeq sequencing of whole body genomic DNA extracted from individual crispants as the method of choice. In combination with CrispRVariants software, we found that this approach provided critically relevant information to confirm that mutagenesis efficiencies of individual sgRNAs are sufficiently high to achieve bi-allelic […]

library_books

CRISPR Cas9 targeted disruption of the yellow ortholog in the housefly identifies the brown body locus

2017
Sci Rep
PMCID: 5496933
PMID: 28676649
DOI: 10.1038/s41598-017-04686-6

[…] CTAATGATGGGCGGATGTGGA.PCR products were purified with the Wizard® Genomic DNA Purification Kit (Promega), subcloned in the pGEM®-T Easy Vector (Promega) and sent for Sanger sequencing (GATA BIOTECH). CrispRVariants and the generation of panel plots was performed from primary sequencing data as previously described, . […]

library_books

Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression

2017
eLife
PMCID: 5389860
PMID: 28350298
DOI: 10.7554/eLife.20728.020

[…] g primers listed in and subject to TA cloning in pcr2.1 (Invitrogen). Plasmid DNA was isolated from individual clones and Sanger sequencing was performed. CRISPR/Cas9 gene editing was analyzed using CrispRVariants (). A T7 Endonuclease I (T7EI) assay was performed using 8 μl of PCR product in 20 µl final reaction containing 2U of T7EI (NEB, Ipswich, MA) for 1 hr at 37°C. Products were analyzed on […]


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CrispRVariants institution(s)
Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; SIB Swiss Insitute of Bioinformatics, University of Zurich, Zurich, Switzerland; Institute of Biochemistry, University of Zurich, Zurich, Switzerland
CrispRVariants funding source(s)
This project was supported by the Canton of Zürich, a Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNSF) professorship (PP00P3_139093), a Marie Curie Career Integration Grant from the European Commission, and a Schweizerische Herzstiftung grant; European Research Council Starting Grant ANTIVIRNA (337284) and an SNSF Project Grant (31003A_149393); a European Commission 7th Framework Collaborative Project RADIANT grant (agreement number 305626) and an SNSF Project Grant (31003A_143883); a Universität Zürich (UZH) URPP Translational Cancer Research Seed Grant; and a UZH Forschungskredit.

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