Package: gsAnalysis 0.0.2

gsAnalysis: Miscellaneous tools for genomic sequence analysis

A miscellaneous toolbox for various genomic sequence analysis tasks. Refer to package vignettes for different topics covered in this package. Part of the y3628 analysis suite.

Authors:Ye Yuan [aut, cre]

gsAnalysis_0.0.2.tar.gz
gsAnalysis_0.0.2.zip(r-4.7-any)gsAnalysis_0.0.2.zip(r-4.6-any)gsAnalysis_0.0.2.zip(r-4.5-any)
gsAnalysis_0.0.2.tgz(r-4.6-any)gsAnalysis_0.0.2.tgz(r-4.5-any)
gsAnalysis_0.0.2.tar.gz(r-4.7-any)gsAnalysis_0.0.2.tar.gz(r-4.6-any)
gsAnalysis_0.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
gsAnalysis/json (API)

# Install 'gsAnalysis' in R:

install.packages('gsAnalysis', repos = c('https://yeyuan98.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yeyuan98/gsanalysis/issues

On CRAN:

cellbiology genetics

2.00 score 1 scripts 15 exports 136 dependencies

Last updated from:0d98b644cb. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	283
source / vignettes	OK	312
linux-release-x86_64	OK	188
macos-release-arm64	OK	111
macos-oldrel-arm64	OK	125
windows-devel-x86_64	OK	148
windows-release-x86_64	OK	133
windows-oldrel-x86_64	OK	130
wasm-release	OK	224

Exports:bam_summary_cigar BranchPointScan diff_breg diff_breg_single IRFinderS_read IRFinderS_readSamples MaxEntScan phastCons readStarGeneCounts RIME rmats_filter rmats_read rmats_toGRange se_subset writeXStringSetNamed

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot broom BSgenome cachem cellranger cigarillo cli clipr codetools colorspace cowplot cpp11 crayon curl DBI DelayedArray Deriv doBy dplyr emmeans estimability farver fastmap forecast formatR fracdiff futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glmmTMB glue gtable hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minqa modelr mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig png prettyunits progress purrr R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppThread RCurl Rdpack readr readxl reformulas rematch restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sandwich scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect timeDate TMB tzdb universalmotif urca utf8 vctrs viridisLite vroom withr XML XVector y3628 yaml zoo

Analysis of common intron properties

Rendered fromintron-properties.Rmdusingknitr::rmarkdown

Last update: 2024-08-11
Started: 2024-08-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
System cell of MaxEntScan perl script	.MaxEntScanRun
Count number of overlapping bases	.overlapWidths
Stranded version of GenomicRanges::shift	.strandedShift
Summarize CIGAR string by addition	bam_summary_cigar
Distance from branchpoint to 3' splicing site	BranchPointScan
Differential analysis with beta regression	diff_breg
Differential analysis with beta regression	diff_breg_single
Read IRFinder-S output of a single sample	IRFinderS_read
Read IRFinder-S output of multiple samples	IRFinderS_readSamples
Splicing site strength scoring by MaxEntScan	MaxEntScan
Conservation scoring by phastCons	phastCons
Read STAR Aligner Gene Counts	readStarGeneCounts
Intron length ratio to mean neighboring exons	RIME
Assign filter labels of rMATS output	rmats_filter
Read rMATS output of different AS patterns	rmats_read
Converts rMATS data frame to GenomicRange	rmats_toGRange
Subset SummarizedExperiment	se_subset
writeXStringSet with identifiers	writeXStringSetNamed