Package: HTSFilter 1.47.0

Andrea Rau

HTSFilter: Filter replicated high-throughput transcriptome sequencing data

This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

Authors:Andrea Rau [cre, aut], Melina Gallopin [ctb], Gilles Celeux [ctb], Florence Jaffrézic [ctb]

HTSFilter_1.47.0.tar.gz
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HTSFilter_1.47.0.tgz(r-4.4-any)HTSFilter_1.47.0.tgz(r-4.3-any)
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HTSFilter.pdf |HTSFilter.html✨
HTSFilter/json (API)
NEWS

# Install 'HTSFilter' in R:

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

Datasets:

sultan - RNA-seq data from humans in Sultan et al.

On BioConductor:HTSFilter-1.45.0(bioc 3.20)HTSFilter-1.44.0(bioc 3.19)

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

sequencing rnaseq preprocessing differentialexpression geneexpression normalization immunooncology

6.23 score 1 packages 56 scripts 406 downloads 35 mentions 3 exports 69 dependencies

Last updated 17 days agofrom:e83b4d005e. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	OK	Oct 30 2024
R-4.3-mac	OK	Oct 31 2024

Exports:HTSBasicFilter HTSFilter normalizeData

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel cli codetools colorspace cpp11 crayon curl DelayedArray DESeq2 edgeR fansi farver formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors scales snow SparseArray statmod SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

HTSFilter package: Quick-start guide

Andrea Rau, Mélina Gallopin, Gilles Celeux, Florence Jaffrézic

Rendered fromHTSFilter.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2020-11-26
Started: 2020-11-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Filter replicated high-throughput transcriptome sequencing data	HTSFilter-package
Implement basic filters for transcriptome sequencing data.	HTSBasicFilter HTSBasicFilter,data.frame-method HTSBasicFilter,DESeqDataSet-method HTSBasicFilter,DGEExact-method HTSBasicFilter,DGEGLM-method HTSBasicFilter,DGEList-method HTSBasicFilter,DGELRT-method HTSBasicFilter,matrix-method
Calculate data-based filtering threshold for replicated transcriptome sequencing data.	HTSFilter HTSFilter,data.frame-method HTSFilter,DESeqDataSet-method HTSFilter,DGEExact-method HTSFilter,DGEGLM-method HTSFilter,DGEList-method HTSFilter,DGELRT-method HTSFilter,matrix-method HTSFilter-methods
Normalize transcriptome sequencing data.	normalizeData
RNA-seq data from humans in Sultan et al. (2008)	sultan