Quick start (tl;dr) | Co-expression analysis with coseq | Transformations for normalized profiles with the Gaussian mixture model | Transformations for normalized profiles with K-means | Model selection | Other options | Running coseq | Exploring coseq results | Running coseq on a DESeq2 or edgeR results object | Customizing coseq graphical outputs | coseq FAQs
Package: coseq 1.37.0
Andrea Rau
coseq: Co-Expression Analysis of Sequencing Data
Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.
Authors:
coseq_1.37.0.tar.gz
coseq_1.37.0.zip(r-4.7)coseq_1.37.0.zip(r-4.6)coseq_1.37.0.zip(r-4.5)
coseq_1.37.0.tgz(r-4.6-any)coseq_1.37.0.tgz(r-4.5-any)
coseq_1.37.0.tar.gz(r-4.7-any)coseq_1.37.0.tar.gz(r-4.6-any)
coseq_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
coseq/json (API)
| # Install 'coseq' in R: |
| install.packages('coseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- fietz - RNA-seq data from the mouse neocortex in Fietz et al.
On BioConductor:coseq-1.37.0(bioc 3.24)coseq-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.
geneexpressionrnaseqsequencingsoftwareimmunooncology
Last updated from:dc85562d8e. Checks:1 WARNING, 7 NOTE, 1 ERROR, 1 OK. Indexed: yes.
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| wasm-release | OK | 184 |
Exports:clusterEntropyclusterInertiaclusterscompareARIcompareICLconvertLegacyCoseqcoseqcoseqFullResultscoseqGlobalPlotscoseqModelPlotscoseqResultscoseqRunDDSEextractDjumpextractICLkmeansProbaPostlikelihoodlogclrmatchContTablemodelnbClusterNormMixClusNormMixClusKNormMixParamplotprobaprofilesshowtcountstransformationTypetransformRNAseq
Dependencies:abindbayesmBHBiobaseBiocGenericsBiocParallelcapusheclassclicodetoolscompositionscorrplotcpp11DelayedArrayDEoptimRDESeq2e1071edgeRfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableHTSClusterHTSFilterIRangesisobandlabelinglambda.rlatticelifecyclelimmalocfitMASSMatrixMatrixGenericsmatrixStatsmvtnormplotrixproxyR6RColorBrewerRcppRcppArmadilloRcppEigenrlangRmixmodrobustbaseS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodSummarizedExperimenttensorAvctrsviridisLitewithrXVector
Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.
coseq package: Quick-start guide
Last update: 2020-12-03
Started: 2016-12-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Co-expression and co-abundance analysis of high-throughput sequencing data | coseq-package |
| Calculation of per-cluster entropy | clusterEntropy |
| Calculation of within-cluster inertia | clusterInertia |
| Pairwise comparisons of ARI values among a set of clustering partitions | compareARI compareARI,coseqResults-method compareARI,data.frame-method compareARI,matrix-method compareARI,RangedSummarizedExperiment-method compareARI-methods |
| Compare corrected ICL values after data transformation | compareICL |
| Convert legacy coseq objects | convertLegacyCoseq |
| Co-expression or co-abudance analysis of high-throughput sequencing data | coseq coseq,data.frame-method coseq,DESeqDataSet-method coseq,matrix-method coseq-methods |
| Accessors for the assigned cluster labels of a coseqResults object. | clusters clusters,coseqResults-method clusters,data.frame-method clusters,matrix-method clusters,RangedSummarizedExperiment-method coseqFullResults coseqFullResults,coseqResults-method DDSEextract DDSEextract,Capushe-method Djumpextract Djumpextract,Capushe-method ICL ICL,coseqResults-method ICL,MixmodCluster-method ICL,NULL-method ICL,RangedSummarizedExperiment-method likelihood likelihood,coseqResults-method likelihood,MixmodCluster-method likelihood,NULL-method likelihood,RangedSummarizedExperiment-method model model,coseqResults-method nbCluster nbCluster,coseqResults-method nbCluster,MixmodCluster-method nbCluster,NULL-method nbCluster,RangedSummarizedExperiment-method proba proba,MixmodCluster-method profiles profiles,coseqResults-method show show,coseqResults-method tcounts tcounts,coseqResults-method transformationType transformationType,coseqResults-method |
| coseqResults object and constructor | coseqResults coseqResults-class |
| Co-expression analysis | coseqRun |
| RNA-seq data from the mouse neocortex in Fietz et al. (2012) | fietz |
| Calculate conditional probabilities of cluster membership for K-means clustering | kmeansProbaPost |
| Calculate the Log Centered Log Ratio (logCLR) transformation | logclr |
| Permute columns of a contingency table | matchContTable |
| Normal mixture model estimation and selection for a series of cluster numbers | NormMixClus |
| Normal mixture model estimation | NormMixClusK |
| Calculate the mean and covariance for a Normal mixture model | NormMixParam |
| Visualize results from coseq clustering | coseqGlobalPlots coseqModelPlots plot plot,coseqResults-method plot-methods |
| Summarize results from coseq clustering | summary summary,coseqResults-method summary-methods |
| Transform RNA-seq data using common transformations | transformRNAseq |
