Package: Cogito 1.19.0

Annika Bürger

Cogito: Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.

Authors:Annika Bürger [cre, aut]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Cogito/json (API)

# Install 'Cogito' in R:

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

Datasets:

MurEpi.ChIP.small - Example data set: Murine ChIP-seq data of GEO GSE77004
MurEpi.RNA.small - Example data set: Murine RNA-seq RPKM values of GSE77004
MurEpi.RRBS.small - Example data set: Murine methylation status data set of GSE77004

On BioConductor:Cogito-1.19.0(bioc 3.24)Cogito-1.18.0(bioc 3.23)

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

functionalgenomics generegulation software sequencing

4.30 score 3 scripts 5 mentions 2 exports 96 dependencies

Last updated from:afc4838f5f. Checks:1 WARNING, 4 OK, 5 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	233
linux-devel-x86_64	OK	449
source / vignettes	OK	288
linux-release-x86_64	OK	371
macos-release-arm64	ERROR	242
macos-oldrel-arm64	ERROR	253
windows-devel	ERROR	322
windows-release	ERROR	329
windows-oldrel	ERROR	327
wasm-release	OK	206

Exports:aggregateRanges summarizeRanges

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bslib cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray digest entropy evaluate farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable highr htmltools httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 rappdirs RColorBrewer RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray SummarizedExperiment sys tinytex TxDb.Mmusculus.UCSC.mm9.knownGene vctrs viridisLite withr xfun XML XVector yaml

Cogito: Compare annotated genomic intervals tool

Introduction | Installation | Workflow | References | Session Information

Rendered fromCogito.Rmdusingknitr::rmarkdown

Last update: 2022-07-07
Started: 2021-08-12

Help page	Topics
Aggregate GRanges with columns of attached values to genes	aggregateRanges
Example data set: Murine ChIP-seq data of GEO GSE77004	MurEpi.ChIP.small
Example data set: Murine RNA-seq RPKM values of GSE77004	MurEpi.RNA.small
Example data set: Murine methylation status data set of GSE77004	MurEpi.RRBS.small
Summarize Aggregated GRanges	summarizeRanges

Package: Cogito 1.19.0

Cogito: Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)