Package: projectR 1.29.0

Genevieve Stein-OBrien

projectR: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.

Authors:Gaurav Sharma, Charles Shin, Jared Slosberg, Loyal Goff, Genevieve Stein-O'Brien

projectR_1.29.0.tar.gz
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projectR_1.29.0.tgz(r-4.6-any)projectR_1.29.0.tgz(r-4.5-any)
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projectR_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
projectR/json (API)

# Install 'projectR' in R:

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

Bug tracker:https://github.com/genesofeve/projectr/issues

Datasets:

AP.RNAseq6l3c3t - CoGAPS patterns and genes weights for p.RNAseq6l3c3t
cr_microglial - CogapsResult object for microglial_counts
CR.RNAseq6l3c3t - CogapsResult object for p.RNAseq6l3c3t
glial_counts - Log-normalized count data from astrocytes and oligodendrocytes in the p6 mouse cortex.
map.ESepiGen4c1l - RNAseqing and ChIPSeq of matched genes in differentiated human iPS cells
map.RNAseq6l3c3t - RNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points
microglial_counts - Log-normalized count data from microglial cells in the p6 mouse cortex.
multivariateAnalysisR_seurat_test - Truncated Seurat Object with latent space projection done to unspecified cells in different stages for multivariateAnalysisR analysis
p.ESepiGen4c1l - RNAseqing and ChIPSeq of matched genes in differentiated human iPS cells
p.RNAseq6l3c3t - RNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points
pd.ESepiGen4c1l - RNAseqing and ChIPSeq of matched genes in differentiated human iPS cells
pd.RNAseq6l3c3t - RNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points
retinal_patterns - CoGAPS patterns learned from the developing mouse retina.

On BioConductor:projectR-1.29.0(bioc 3.24)projectR-1.28.0(bioc 3.23)

functionalprediction generegulation biologicalquestion software

8.38 score 65 stars 123 scripts 2 mentions 16 exports 104 dependencies

Last updated from:c02488b01a. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	247
linux-devel-x86_64	NOTE	388
source / vignettes	OK	389
linux-release-x86_64	NOTE	442
macos-release-arm64	NOTE	197
macos-oldrel-arm64	NOTE	234
windows-devel	NOTE	291
windows-release	NOTE	214
windows-oldrel	NOTE	293
wasm-release	OK	227

Exports:alluvialMat aucMat cluster2pattern clusterPlotR correlateR geneMatchR getTSNE getUMAP intersectoR multivariateAnalysisR pdVolcano plotConfidenceIntervals plotVolcano projectionDriveR projectR rotatoR

Dependencies:abind askpass assertthat babelgene BH Biobase BiocGenerics BiocManager BiocParallel bitops caTools cli cluster codetools colorspace cowplot cpp11 curl data.table DelayedArray digest doParallel dplyr farver fastmatch fgsea foreach formatR futile.logger futile.options generics GenomicRanges ggalluvial ggplot2 ggrepel glue gplots gridBase gridExtra gtable gtools here IRanges isoband iterators jsonlite KernSmooth labeling lambda.r lattice lazyeval lifecycle limma magrittr Matrix MatrixGenerics MatrixModels matrixStats msigdbr NMF openssl pillar pkgconfig plyr png purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RcppTOML registry reshape2 reticulate rlang rngtools ROCR rprojroot RSpectra S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tsne umap utf8 vctrs viridis viridisLite withr XVector

projectR Vignette

Rendered fromprojectR.Rmdusingknitr::rmarkdown

Last update: 2024-02-21
Started: 2017-10-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
alluvialMat	alluvialMat
CoGAPS patterns and genes weights for p.RNAseq6l3c3t	AP.RNAseq6l3c3t
aucMat	aucMat
bonferroniCorrectedDifferences	bonferroniCorrectedDifferences
Generic cluster2pattern function	cluster2pattern cluster2pattern,character-method cluster2pattern,hclust-method cluster2pattern,kmeans-method cluster2pattern,numeric-method
cluster2pattern	cluster2pattern-class
Generic clusterPlotR function	clusterPlotR clusterPlotR,ANY,hclust-method clusterPlotR,ANY,kmeans-method
correlateR	correlateR
correlateR	correlateR-class
CogapsResult object for microglial_counts	cr_microglial
CogapsResult object for p.RNAseq6l3c3t	CR.RNAseq6l3c3t
Generic geneMatchR function	geneMatchR
getTSNE	getTSNE
getUMAP	getUMAP
log-normalized count data from astrocytes and oligodendrocytes in the p6 mouse cortex.	glial_counts
Constructor for cluster2pattern	initialize,cluster2pattern-method
Constructor for correlateR	initialize,correlateR-method
Constructor for rotatoR	initialize,rotatoR-method
Generic intersectoR function	intersectoR intersectoR,hclust,hclust-method intersectoR,kmeans,kmeans-method
RNAseqing and ChIPSeq of matched genes in differentiated human iPS cells	map.ESepiGen4c1l
RNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points	map.RNAseq6l3c3t
log-normalized count data from microglial cells in the p6 mouse cortex.	microglial_counts
Generic multivariateAnalysisR function	multivariateAnalysisR
Truncated Seurat Object with latent space projection done to unspecified cells in different stages for multivariateAnalysisR analysis	multivariateAnalysisR_seurat_test
RNAseqing and ChIPSeq of matched genes in differentiated human iPS cells	p.ESepiGen4c1l
RNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points	p.RNAseq6l3c3t
RNAseqing and ChIPSeq of matched genes in differentiated human iPS cells	pd.ESepiGen4c1l
RNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points	pd.RNAseq6l3c3t
pdVolcano	pdVolcano
plotConfidenceIntervals	plotConfidenceIntervals
plotVolcano	plotVolcano
projectionDriveR	projectionDriveR
Generic projectR function	projectR projectR,dgCMatrix,matrix-method projectR,matrix,cluster2pattern-method projectR,matrix,correlateR-method projectR,matrix,hclust-method projectR,matrix,kmeans-method projectR,matrix,LinearEmbeddingMatrix-method projectR,matrix,matrix-method projectR,matrix,prcomp-method projectR,matrix,rotatoR-method
CoGAPS patterns learned from the developing mouse retina.	retinal_patterns
rotatoR	rotatoR
rotatoR	rotatoR-class