Package: HTSCluster 2.0.11

HTSCluster: Clustering High-Throughput Transcriptome Sequencing (HTS) Data

A Poisson mixture model is implemented to cluster genes from high- throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).

Authors:Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis- Rabusseau

HTSCluster_2.0.11.tar.gz
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HTSCluster.pdf |HTSCluster.html✨
HTSCluster/json (API)
NEWS

# Install 'HTSCluster' in R:

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

Bug tracker:https://github.com/andreamrau/htscluster/issues

On CRAN:

13 exports 2.24 score 8 dependencies 1 dependents 7 mentions 7 scripts 433 downloads

Last updated 1 years agofrom:ca2ab810ac. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 31 2024
R-4.5-win	OK	Aug 31 2024
R-4.5-linux	OK	Aug 31 2024
R-4.4-win	OK	Aug 31 2024
R-4.4-mac	OK	Aug 31 2024
R-4.3-win	OK	Aug 31 2024
R-4.3-mac	OK	Aug 31 2024

Exports:emInit highDimensionARI HTSClusterUsersGuide kmeanInit logLikePoisMix logLikePoisMixDiff PoisMixClus PoisMixClusWrapper PoisMixMean PoisMixSim probaPost probaPostInit splitEMInit

Dependencies:capushe edgeR lattice limma locfit MASS plotrix statmod

Co-expression analysis of RNA-seq data with the "HTSCluster" package

Rendered fromHTSCluster.Rnwusingutils::Sweaveon Aug 31 2024.

Last update: 2018-09-11
Started: 2018-09-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Clustering high throughput sequencing (HTS) data	HTSCluster-package HTSCluster
Calculate ARI for high-dimensional data via data splits	highDimensionARI
View HTSCluster User's Guide	HTSClusterUsersGuide
Parameter initialization for a Poisson mixture model.	emInit kmeanInit probaPostInit splitEMInit
Log likelihood calculation for a Poisson mixture model	logLikePoisMix logLikePoisMixDiff mylogLikePoisMixObs
Visualize results from clustering using a Poisson mixture model	plot.HTSCluster plot.HTSClusterWrapper
Poisson mixture model estimation and model selection	PoisMixClus PoisMixClusWrapper
Calculate the conditional per-cluster mean of each observation	PoisMixMean
Simulate data from a Poisson mixture model	PoisMixSim
Calculate the conditional probability of belonging to each cluster in a Poisson mixture model	probaPost
Summarize results from clustering using a Poisson mixture model	summary.HTSCluster summary.HTSClusterWrapper