Package: GUIDEseq 1.42.0

Lihua Julie Zhu

GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.

Authors:Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Hervé Pagès , Alper Kucukural, Manuel Garber, Scot A. Wolfe

GUIDEseq_1.42.0.tar.gz
GUIDEseq_1.42.0.zip(r-4.7-any)GUIDEseq_1.42.0.zip(r-4.6-any)GUIDEseq_1.42.0.zip(r-4.5-any)
GUIDEseq_1.42.0.tgz(r-4.6-any)GUIDEseq_1.42.0.tgz(r-4.5-any)
GUIDEseq_1.42.0.tar.gz(r-4.7-any)GUIDEseq_1.42.0.tar.gz(r-4.6-any)
GUIDEseq_1.42.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GUIDEseq/json (API)

# Install 'GUIDEseq' in R:

install.packages('GUIDEseq', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

peaks.gr - Example cleavage sites
uniqueCleavageEvents - Example unique cleavage sites

On BioConductor:GUIDEseq-1.43.1(bioc 3.24)GUIDEseq-1.42.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology generegulation sequencing workflowstep crispr

4.26 score 23 scripts 434 downloads 4 mentions 15 exports 169 dependencies

Last updated from:39caeff59b (on RELEASE_3_23). Checks:1 FAILURE, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	FAILURE	375
linux-devel-x86_64	NOTE	802
source / vignettes	OK	561
linux-release-x86_64	NOTE	739
macos-release-arm64	NOTE	369
macos-oldrel-arm64	NOTE	544
windows-devel	NOTE	585
windows-release	NOTE	666
windows-oldrel	NOTE	657
wasm-release	OK	339

Exports:annotateOffTargets buildFeatureVectorForScoringBulge combineOfftargets createBarcodeFasta getBestAlnInfo getPeaks getUniqueCleavageEvents getUsedBarcodes GUIDEseqAnalysis mergePlusMinusPeaks offTargetAnalysisOfPeakRegions offTargetAnalysisWithBulge PEtagAnalysis plotAlignedOfftargets plotTracks

Dependencies:abind ade4 AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO biocmake BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem cellranger ChIPpeakAnno cigarillo cli clipr codetools config cpp11 crayon CRISPRseek curl data.table DBI dbplyr DelayedArray dir.expiry dplyr ensembldb farver fastmap filelock forcats foreign formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue graph gtable gtools hash haven here hms httr httr2 InteractionSet IRanges isoband jsonlite KEGGREST keras labeling lambda.r lattice lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mime mltools multtest nlme openssl openxlsx patchwork pillar pixmap pkgconfig png prettyunits processx progress ProtGenerics ps purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppThread RcppTOML RCurl readr readxl regioneR rematch restfulr reticulate rhdf5 rhdf5filters Rhdf5lib Rhtslib rio rjson rlang rprojroot Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 scales segmented Seqinfo seqinr snow sp SparseArray statmod stringi stringr SummarizedExperiment survival sys tensorflow tfautograph tfruns tibble tidyr tidyselect tzdb UCSC.utils universalmotif utf8 vctrs VennDiagram viridisLite vroom whisker withr writexl XML xml2 XVector yaml zeallot zip

GUIDEseq Vignette

1 Introduction | 2 Workflow of GUIDE-seq data analysis | 3 References | 4 Session Info

Rendered fromGUIDEseq.Rnwusingutils::Sweave

Last update: 2024-03-18
Started: 2015-10-06

Help page	Topics
Analysis of GUIDE-seq	GUIDEseq-package GUIDEseq
Annotate offtargets with gene name	annotateOffTargets
Build Feature Vector For Scoring Offtargets with Bulge	buildFeatureVectorForScoringBulge
Combine Offtargets	combineOfftargets
Compare Samples using Fisher's exact test	compareSamples
Create barcode as fasta file format for building bowtie1 index	createBarcodeFasta
Parse pairwise alignment	getBestAlnInfo
Obtain peaks from GUIDE-seq	getPeaks
Using UMI sequence to obtain the starting sequence library	getUniqueCleavageEvents
Create barcodes from the p5 and p7 index used for each sequencing lane	getUsedBarcodes
Analysis pipeline for GUIDE-seq dataset	GUIDEseqAnalysis
Merge peaks from plus strand and minus strand	mergePlusMinusPeaks
Offtarget Analysis of GUIDE-seq peaks	offTargetAnalysisOfPeakRegions
offTarget Analysis With Bulges Allowed Finding offtargets around peaks from GUIDE-seq or around any given genomic regions with bulges allowed in gRNA or the DNA sequence of offTargets when aligning gRNA and DNA sequences.	offTargetAnalysisWithBulge
example cleavage sites	peaks.gr
Analysis pipeline for PEtag-seq dataset	PEtagAnalysis
Plot offtargets aligned to the target sequence	plotAlignedOfftargets
Plot offtargets from multiple samples as heatmap	plotHeatmapOfftargets
Plot offtargets as manhantann plots or along all chromosomes with one track per chromosome, or scatter plot for two selected measurements	plotTracks
example unique cleavage sites	uniqueCleavageEvents

Package: GUIDEseq 1.42.0

GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

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Help Manual

Usage by other packages (reverse dependencies)