Package: TCseq 1.37.0

Mengjun Wu

TCseq: Time course sequencing data analysis

Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data.

Authors:Mengjun Wu <[email protected]>, Lei Gu <[email protected]>

TCseq_1.37.0.tar.gz
TCseq_1.37.0.zip(r-4.7)TCseq_1.37.0.zip(r-4.6)TCseq_1.37.0.zip(r-4.5)
TCseq_1.37.0.tgz(r-4.6-any)TCseq_1.37.0.tgz(r-4.5-any)
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TCseq_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
TCseq/json (API)

# Install 'TCseq' in R:

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

Datasets:

countsTable - An example read Counts table
experiment - An example experiment design without BAM file infomration
experiment_BAMfile - An example experiment design with BAM file infomration
genomicIntervals - An example reference genomic regions
tca_ATAC - An example TCA object

On BioConductor:TCseq-1.37.0(bioc 3.24)TCseq-1.36.0(bioc 3.23)

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

epigenetics timecourse sequencing chipseq rnaseq differentialexpression clustering visualization

5.76 score 58 scripts 17 mentions 20 exports 64 dependencies

Last updated from:243c705c3a. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	183
linux-devel-x86_64	WARNING	334
source / vignettes	OK	275
linux-release-x86_64	WARNING	385
macos-release-arm64	WARNING	240
macos-oldrel-arm64	WARNING	191
windows-devel	WARNING	243
windows-release	WARNING	257
windows-oldrel	WARNING	260
wasm-release	OK	179

Exports:clustCenters clustCluster clustData clustMembership clustResults countReads counts counts<-DBanalysis DBresult DBresult.cluster design genomicFeature peakreference TCA TCAFromSummarizedExperiment tcTable timeclust timeclustplot timecourseTable

Dependencies:abind BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo class cli cluster codetools cpp11 crayon DelayedArray e1071 edgeR farver formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable IRanges isoband labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats plyr proxy R6 RColorBrewer Rcpp reshape2 Rhtslib rlang Rsamtools S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment vctrs viridisLite withr XVector

TCseq Vignette

Rendered fromTCseq.Rnwusingutils::Sweave

Last update: 2023-09-11
Started: 2016-11-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
clust class	clust clust-class
Accessors to extract slots of a clust class.	clust.accessors clustCenters clustCenters,clust-method clustCluster clustCluster,clust-method clustData clustData,clust-method clustMembership clustMembership,clust-method
count mapped reads overlap genomic intervals	countReads
Extracts counts of a TCA object.	counts counts,TCA-method counts<-,TCA-method
An example read Counts table	countsTable
Perform differential expression analysis	DBanalysis
This function tests for differential expression	DBresult DBresult.cluster
An example experiment design without BAM file infomration	experiment
An example experiment design with BAM file infomration	experiment_BAMfile
An example reference genomic regions	genomicIntervals
combine and merge multiple BED files	peakreference
An example TCA object	tca_ATAC
TCA class and constructor	TCA TCA-class TCAFromSummarizedExperiment
Accessors to extract slots of a TCA class.	clustResults clustResults,TCA-method design design,TCA-method genomicFeature genomicFeature,TCA-method TCA.accessors tcTable tcTable,TCA-method
time couse data clustering	timeclust
Plot clustering results for time course data.	timeclustplot
constructs time course table for clustering analysis	timecourseTable