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

Download


Versioning


Add your version

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 in publications

 (7)
PMCID: 5884836
PMID: 29618800
DOI: 10.1038/s41598-018-24036-4

[…] 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 […]

PMCID: 5940144
PMID: 29511025
DOI: 10.1534/g3.117.300396

[…] and 24 i7 indexes (n701-n729) enabling multiplexing of 384 individual libraries. sr 100 bp or pe 150 sequencing was done on an illumina hs3000 or hs4000 platform. sequence analysis was done using crisprvariants ()., given the recent concerns of index switching during sequencing of dual index multiplexed samples using illumina platforms (), the pooled libraries were treated with exonuclease […]

PMCID: 5897731
PMID: 29590639
DOI: 10.1242/dmm.033027

[…] miseq 300 at the sequencing center of purdue university. raw reads have been deposited to the sequence read archive (accession number srp132222). mutational efficiency was calculated using the crisprvariants r package (lindsay et al., 2016), with the specific code below to compare aligned reads and count read frequencies:, crispr_set <- […]

PMCID: 5799254
PMID: 29402884
DOI: 10.1038/s41467-017-02349-8

[…] paired reads were trimmed, filtered, and then aligned to the reference amplicon in geneious (v9, biomatters). to obtain haplotypes present in drug-resistant samples, bam files were analyzed with the crisprvariants package run in rstudio by defining a 35–140 bp spanning region across the endonuclease cut site, as defined by pre-analysis of localized variants within geneious. for this purpose, […]

PMCID: 5577161
PMID: 28855635
DOI: 10.1038/s41598-017-10347-5

[…] (agilent technologies) and subcloned using strataclone pcr cloning kit (agilent technologies). positive clones were sequenced by sanger method and abi 310 automated sequencer (applied biosystems). crisprvariants and panel plots were compiled from primary sanger sequencing data as described in lindsay et al.as well as using new functionality to display duplex guide pairs (e.g., fig. ) […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

CrispRVariants reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CrispRVariants