Package: TCseq 1.31.0

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]>

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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:

On BioConductor:TCseq-1.31.0(bioc 3.21)TCseq-1.30.0(bioc 3.20)

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

epigeneticstimecoursesequencingchipseqrnaseqdifferentialexpressionclusteringvisualization

5.45 score 28 scripts 574 downloads 17 mentions 20 exports 80 dependencies

Last updated 4 months agofrom:2ff417ddf6. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-winWARNINGJan 29 2025
R-4.5-macWARNINGJan 29 2025
R-4.5-linuxWARNINGJan 29 2025
R-4.4-winWARNINGJan 29 2025
R-4.4-macWARNINGJan 29 2025
R-4.3-winWARNINGJan 29 2025
R-4.3-macWARNINGJan 29 2025

Exports:clustCentersclustClusterclustDataclustMembershipclustResultscountReadscountscounts<-DBanalysisDBresultDBresult.clusterdesigngenomicFeaturepeakreferenceTCATCAFromSummarizedExperimenttcTabletimeclusttimeclustplottimecourseTable

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclasscliclustercodetoolscolorspacecpp11crayoncurlDelayedArraye1071edgeRfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrproxyR6RColorBrewerRcppreshape2RhtslibrlangRsamtoolsS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVector

TCseq Vignette

Rendered fromTCseq.Rnwusingutils::Sweaveon Jan 29 2025.

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

Readme and manuals

Help Manual

Help pageTopics
clust classclust 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 intervalscountReads
Extracts counts of a TCA object.counts counts,TCA-method counts<-,TCA-method
An example read Counts tablecountsTable
Perform differential expression analysisDBanalysis
This function tests for differential expressionDBresult DBresult.cluster
An example experiment design without BAM file infomrationexperiment
An example experiment design with BAM file infomrationexperiment_BAMfile
An example reference genomic regionsgenomicIntervals
combine and merge multiple BED filespeakreference
An example TCA objecttca_ATAC
TCA class and constructorTCA 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 clusteringtimeclust
Plot clustering results for time course data.timeclustplot
constructs time course table for clustering analysistimecourseTable