Package: isoformic 0.1.1.9003

isoformic: Isoform-Level Biological Interpretation of Transcriptomic Data

Isoform-level biological interpretation of transcriptomic data.

Authors:Lucio Rezende Queiroz [aut, cre, cph], Izabela Mamede Conceicao [aut, ctb], Luigi Marchionni [aut, ctb], Gloria Franco [aut, ctb]

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

# Install 'isoformic' in R:

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

Bug tracker:https://github.com/luciorq/isoformic/issues

On CRAN:

bioconductor bioinformatics transcriptomics

4.00 score 20 stars 2 scripts 11 exports 91 dependencies

Last updated 12 days agofrom:b61feebf73. Checks:ERROR: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 11 2024
R-4.5-win	ERROR	Nov 11 2024
R-4.5-linux	ERROR	Nov 11 2024
R-4.4-win	ERROR	Nov 11 2024
R-4.4-mac	ERROR	Nov 11 2024
R-4.3-win	ERROR	Nov 11 2024
R-4.3-mac	ERROR	Nov 11 2024

Exports:download_reference is_deg_sig join_DEG_DET make_tx_to_gene plot_log2FC plot_tx_context plot_tx_expr prepare_annotation prepare_exon_annotation prepare_profile_data run_enrichment

Dependencies:abind backports BH BiocParallel bit bit64 boot broom car carData cli clipr codetools colorspace corrplot cowplot cpp11 crayon data.table Deriv doBy dplyr fansi farver fastmatch fgsea forcats formatR Formula fs futile.logger futile.options generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable hms isoband labeling lambda.r lattice lifecycle lme4 magrittr MASS Matrix MatrixModels mgcv microbenchmark minqa modelr munsell nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig polynom prettyunits progress purrr quantreg R6 RColorBrewer Rcpp RcppEigen readr rlang rstatix scales snow SparseM stringi stringr survival tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Download Reference Files from GENCODE	download_reference
Annotate Transcripts with Differential Gene Expression Significance	is_deg_sig
Merge Gene and Transcript Level Differential Expression Tables	join_DEG_DET
Create Transcript-to-Gene Relationship Table	make_tx_to_gene
Plot Log2 Fold-Change Results for Selected Genes	plot_log2FC
Plot Transcript Genomic Context	plot_tx_context
Plot Transcript per gene expression	plot_tx_expr
Prepare Annotation	prepare_annotation
Prepare Exon based Position Annotation Table	prepare_exon_annotation
Prepare Data for Gene and Transcript Expression Profile Plot	prepare_profile_data
Run Gene Set Enrichment Analysis for Different Transcript Types	run_enrichment

Usage by other packages (reverse dependencies)