Package: TCseq 1.29.0

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_1.29.0.tar.gz
TCseq_1.29.0.zip(r-4.5)TCseq_1.29.0.zip(r-4.4)TCseq_1.29.0.zip(r-4.3)
TCseq_1.29.0.tgz(r-4.4-any)TCseq_1.29.0.tgz(r-4.3-any)
TCseq_1.29.0.tar.gz(r-4.5-noble)TCseq_1.29.0.tar.gz(r-4.4-noble)
TCseq_1.29.0.tgz(r-4.4-emscripten)TCseq_1.29.0.tgz(r-4.3-emscripten)
TCseq.pdf |TCseq.html✨
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-1.29.0(bioc 3.20)TCseq-1.28.0(bioc 3.19)

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

bioconductor-package

20 exports 1.08 score 80 dependencies 17 mentions

Last updated 2 months agofrom:1de767b83b

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

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops class cli cluster codetools colorspace cpp11 crayon curl DelayedArray e1071 edgeR fansi farver formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr proxy R6 RColorBrewer Rcpp reshape2 Rhtslib rlang Rsamtools S4Arrays S4Vectors scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

TCseq Vignette

Rendered fromTCseq.Rnwusingutils::Sweaveon Jun 27 2024.

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