Package: Cogito 1.11.0

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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Cogito.pdf |Cogito.html✨
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# 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-1.11.0(bioc 3.20)Cogito-1.10.0(bioc 3.19)

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

bioconductor-package

2 exports 0.49 score 105 dependencies 5 mentions

Last updated 2 months agofrom:acf728d565

Exports:aggregateRanges summarizeRanges

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bslib cachem cli codetools colorspace cpp11 crayon curl DBI DelayedArray digest entropy evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable highr htmltools httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png R6 rappdirs RColorBrewer RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales snow SparseArray SummarizedExperiment sys tibble tinytex TxDb.Mmusculus.UCSC.mm9.knownGene UCSC.utils utf8 vctrs viridisLite withr xfun XML XVector yaml zlibbioc

Cogito: Compare annotated genomic intervals tool

Annika Buerger

Rendered fromCogito.Rmdusingknitr::rmarkdownon Jun 15 2024.

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 1.11.0

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

Cogito: Compare annotated genomic intervals tool

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)