Package: qsvaR 1.11.1

Hedia Tnani

qsvaR: Generate Quality Surrogate Variable Analysis for Degradation Correction

The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.

Authors:Joshua Stolz [aut], Hedia Tnani [ctb, cre], Leonardo Collado-Torres [ctb], Nicholas J. Eagles [aut]

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qsvaR.pdf |qsvaR.html✨
qsvaR/json (API)
NEWS

# Install 'qsvaR' in R:

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

Bug tracker:https://github.com/lieberinstitute/qsvar/issues

Datasets:

degradation_tstats - Degradation time t-statistics
rse_tx - Example of RSE object with RNA-seq transcript quantification data
transcripts - Transcripts for Degradation Models

On BioConductor:qsvaR-1.11.0(bioc 3.21)qsvaR-1.10.0(bioc 3.20)

software workflowstep normalization biologicalquestion differentialexpression sequencing coverage bioconductor brain degradation human qsva

5.43 score 4 scripts 372 downloads 9 exports 88 dependencies

Last updated 11 days agofrom:55f85137fa. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 11 2024
R-4.5-win	NOTE	Dec 11 2024
R-4.5-linux	NOTE	Dec 11 2024
R-4.4-win	NOTE	Dec 11 2024
R-4.4-mac	NOTE	Dec 11 2024
R-4.3-win	NOTE	Dec 11 2024
R-4.3-mac	NOTE	Dec 11 2024

Exports:DEqual get_qsvs getDegTx getPCs k_qsvs normalize_tx_names qSVA select_transcripts which_tx_names

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools colorspace cpp11 crayon curl DBI DelayedArray dplyr edgeR fansi farver fastmap formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png R6 RColorBrewer rlang RSQLite S4Arrays S4Vectors scales snow SparseArray statmod SummarizedExperiment survival sva sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML xtable XVector zlibbioc

Introduction to qsvaR

Joshua M. Stolz, Hedia Tnani, Leonardo Collado-Torres

Rendered fromIntro_qsvaR.Rmdusingknitr::rmarkdownon Dec 11 2024.

Last update: 2024-11-26
Started: 2021-12-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Degradation time t-statistics	degradation_tstats
Differential expression quality (DEqual) plot	DEqual
Generate matrix of qsvs	get_qsvs
Obtain expression matrix for degraded transcripts	getDegTx
PCs from transcripts	getPCs
Apply num.sv algorithm to determine the number of pcs to be included	k_qsvs
Remove version number from Gencode/Ensembl transcript names	normalize_tx_names
A wrapper function used to perform qSVA in one step.	qSVA
Example of RSE object with RNA-seq transcript quantification data	rse_tx
Select transcripts associated with degradation	select_transcripts
Transcripts for Degradation Models	transcripts
Check validity of transcript vectors and return a vector matching indexes in tx1	which_tx_names