Package: transcriptogramer 1.35.0

Diego Morais

transcriptogramer: Transcriptional analysis based on transcriptograms

R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.

Authors:Diego Morais [aut, cre], Rodrigo Dalmolin [aut]

transcriptogramer_1.35.0.tar.gz
transcriptogramer_1.35.0.zip(r-4.7)transcriptogramer_1.35.0.zip(r-4.6)transcriptogramer_1.35.0.zip(r-4.5)
transcriptogramer_1.35.0.tgz(r-4.6-any)transcriptogramer_1.35.0.tgz(r-4.5-any)
transcriptogramer_1.35.0.tar.gz(r-4.7-any)transcriptogramer_1.35.0.tar.gz(r-4.6-any)
transcriptogramer_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
transcriptogramer/json (API)

# Install 'transcriptogramer' in R:

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

Bug tracker:https://github.com/arthurvinx/transcriptogramer/issues

Datasets:

association - Association
DEsymbols - Dictionary Protein2Symbol
GPL570 - Dictionary Protein2Probe
GSE9988 - Dataset containing expression values
Hs700 - Ordered Homo sapiens proteins of combined score greater than or equal to 700
Hs800 - Ordered Homo sapiens proteins of combined score greater than or equal to 800
Hs900 - Ordered Homo sapiens proteins of combined score greater than or equal to 900
HsBPTerms - Dictionary Protein2GO
Mm700 - Ordered Mus musculus proteins of combined score greater than or equal to 700
Mm800 - Ordered Mus musculus proteins of combined score greater than or equal to 800
Mm900 - Ordered Mus musculus proteins of combined score greater than or equal to 900
Rn700 - Ordered Rattus norvegicus proteins of combined score greater than or equal to 700
Rn800 - Ordered Rattus norvegicus proteins of combined score greater than or equal to 800
Rn900 - Ordered Rattus norvegicus proteins of combined score greater than or equal to 900
Sc700 - Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700
Sc800 - Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800
Sc900 - Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900

On BioConductor:transcriptogramer-1.35.0(bioc 3.24)transcriptogramer-1.34.0(bioc 3.23)

software network visualization systemsbiology geneexpression genesetenrichment graphandnetwork clustering differentialexpression microarray rnaseq transcription immunooncology

4.81 score 4 stars 9 scripts 2 mentions 13 exports 82 dependencies

Last updated from:d14dd1a876. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	196
linux-devel-x86_64	OK	299
source / vignettes	OK	741
linux-release-x86_64	OK	334
macos-release-arm64	OK	158
macos-oldrel-arm64	OK	152
windows-devel	OK	213
windows-release	OK	224
windows-oldrel	OK	213
wasm-release	OK	158

Exports:clusterEnrichment clusterVisualization connectivityProperties DE differentiallyExpressed enrichmentPlot orderingProperties radius radius<-Terms transcriptogramPreprocess transcriptogramStep1 transcriptogramStep2

Dependencies:AnnotationDbi askpass Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl data.table DBI dbplyr doSNOW dplyr farver fastmap filelock foreach generics ggplot2 glue GO.db graph gtable hms httr httr2 igraph IRanges isoband iterators jsonlite KEGGREST labeling lattice lifecycle limma magrittr Matrix matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer RedeR rlang RSQLite S4Vectors S7 scales Seqinfo snow SparseM statmod stringi stringr sys tibble tidyr tidyselect topGO utf8 vctrs viridisLite withr xml2 XVector

The transcriptogramer user's guide

Rendered fromtranscriptogramer.Rmdusingknitr::rmarkdown

Last update: 2020-11-19
Started: 2017-10-02

Help page	Topics
Transcriptional analysis based on transcriptograms	transcriptogramer-package transcriptogramer
Association	association
Term enrichment	clusterEnrichment clusterEnrichment,Transcriptogram-method clusterEnrichment-method
Displays graphs of the differentially expressed clusters	clusterVisualization clusterVisualization,Transcriptogram-method clusterVisualization-method
Calculates average graph properties as function of node connectivity	connectivityProperties connectivityProperties,Transcriptogram-method connectivityProperties-method
Get DE	DE DE,Transcriptogram-method DE-method
Dictionary Protein2Symbol	DEsymbols
Identify which genes are differentially expressed	differentiallyExpressed differentiallyExpressed,Transcriptogram-method differentiallyExpressed-method
Projects Gene Ontology terms on the ordering	enrichmentPlot enrichmentPlot,Transcriptogram-method enrichmentPlot-method
Dictionary Protein2Probe	GPL570
Dataset containing expression values	GSE9988
Ordered Homo sapiens proteins of combined score greater than or equal to 700	Hs700
Ordered Homo sapiens proteins of combined score greater than or equal to 800	Hs800
Ordered Homo sapiens proteins of combined score greater than or equal to 900	Hs900
Dictionary Protein2GO	HsBPTerms
Ordered Mus musculus proteins of combined score greater than or equal to 700	Mm700
Ordered Mus musculus proteins of combined score greater than or equal to 800	Mm800
Ordered Mus musculus proteins of combined score greater than or equal to 900	Mm900
Calculates graph properties projected on the ordered proteins	orderingProperties orderingProperties,Transcriptogram-method orderingProperties-method
Radius	radius radius,Transcriptogram-method radius-method radius<- radius<-,Transcriptogram-method
Ordered Rattus norvegicus proteins of combined score greater than or equal to 700	Rn700
Ordered Rattus norvegicus proteins of combined score greater than or equal to 800	Rn800
Ordered Rattus norvegicus proteins of combined score greater than or equal to 900	Rn900
Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700	Sc700
Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800	Sc800
Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900	Sc900
Get terms	Terms Terms,Transcriptogram-method Terms-method
Class Transcriptogram	Transcriptogram-class
Creates an object of class Transcriptogram	transcriptogramPreprocess
Calculates the average of the expression values related to the same protein	transcriptogramStep1 transcriptogramStep1,Transcriptogram-method transcriptogramStep1-method
Calculates the average of the expression values using a sliding window	transcriptogramStep2 transcriptogramStep2,Transcriptogram-method transcriptogramStep2-method

Package: transcriptogramer 1.35.0

transcriptogramer: Transcriptional analysis based on transcriptograms

Citation

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Help Manual

Usage by other packages (reverse dependencies)