Package: InTAD 1.33.0

Konstantin Okonechnikov

InTAD: Search for correlation between epigenetic signals and gene expression in TADs

The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.

Authors:Konstantin Okonechnikov, Serap Erkek, Lukas Chavez

InTAD_1.33.0.tar.gz
InTAD_1.33.0.zip(r-4.7)InTAD_1.33.0.zip(r-4.6)InTAD_1.33.0.zip(r-4.5)
InTAD_1.33.0.tgz(r-4.6-any)InTAD_1.33.0.tgz(r-4.5-any)
InTAD_1.33.0.tar.gz(r-4.7-any)InTAD_1.33.0.tar.gz(r-4.6-any)
InTAD_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
InTAD/json (API)

# Install 'InTAD' in R:

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

Datasets:

enhSel - Enhancer signals subset detected from medulloblatoma samples
enhSelGR - Genomic coordiantes of enhancer signals subet
loopsDfSel - Data frame containing coordinates of loops
mbAnnData - Data frame containing information about samples
rpkmCountsSel - Gene expression subset from medulloblastoma samples
tadGR - Genomic coordiantes of topologically associated domains
txsSel - Genomic coordiantes of genes subset

On BioConductor:InTAD-1.33.0(bioc 3.24)InTAD-1.32.0(bioc 3.23)

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

epigenetics sequencing chipseq rnaseq hic geneexpression immunooncology

4.30 score 7 scripts 2 mentions 13 exports 124 dependencies

Last updated from:110b26b43c. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	215
linux-devel-x86_64	OK	455
source / vignettes	OK	313
linux-release-x86_64	OK	429
macos-release-arm64	OK	205
macos-oldrel-arm64	OK	241
windows-devel	OK	254
windows-release	OK	328
windows-oldrel	OK	349
wasm-release	OK	202

Exports:combineInTAD combineWithLoops exprs filterGeneExpr findCorFromLoops findCorrelation geneCoords loadSigInTAD newSigInTAD plotCorAcrossRef plotCorrelation sigCoords signals

Dependencies:abind askpass backports BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops boot broom car carData cigarillo cli codetools colorspace corrplot cowplot cpp11 crayon curl DelayedArray Deriv doBy dplyr farver forecast formatR Formula fracdiff futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mclust mgcv mime minqa modelr MultiAssayExperiment nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig plyr polynom purrr quantreg qvalue R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas reshape2 restfulr Rhtslib rjson rlang Rsamtools rstatix rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr XML XVector yaml zoo

Correlation of epigenetic signals and genes in TADs

Rendered fromInTAD.Rmdusingknitr::rmarkdown

Last update: 2020-09-06
Started: 2018-03-19

Help page	Topics
Preparation for correlation analysis	combineInTAD
Preparation for correlation analysis via loops	combineWithLoops
Enhancer signals subset detected from medulloblatoma samples	enhSel
Genomic coordiantes of enhancer signals subet	enhSelGR
Gene expression counts table	exprs,InTADSig-method
Function to filter gene expression	filterGeneExpr
Function to perfrom correlation analysis via loops.	findCorFromLoops
Function to perfrom correlation analysis in TADs	findCorrelation
Preparation for correlation analysis for a signal	fnSE
Gene coords GRanges	geneCoords geneCoords,InTADSig-method
Function to estimate gene expression	get.enr.bg.normfit
The InTADSig Class	InTADSig InTADSig-class
Load InTADSig object from text files	loadSigInTAD
Data frame containing coordinates of loops	loopsDfSel
Data frame containing information about samples	mbAnnData
Create InTADSig object	newSigInTAD
Function to plot correlation across genome	plotCorAcrossRef
Function to plot correlation	plotCorrelation
Gene expression subset from medulloblastoma samples	rpkmCountsSel
Signal coords GRanges	sigCoords sigCoords,InTADSig-method
Signal values table	signals signals,InTADSig-method
Genomic coordiantes of topologically associated domains	tadGR
Genomic coordiantes of genes subset	txsSel

Package: InTAD 1.33.0

InTAD: Search for correlation between epigenetic signals and gene expression in TADs

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