Package: isoformic 0.1.2.9019

isoformic: Isoform-Level Biological Interpretation of Transcriptomic Data

Isoform-level biological interpretation of transcriptomic data.

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

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

# 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

Pkgdown/docs site:https://luciorq.github.io

On CRAN:

bioconductor bioinformatics transcriptomics

4.37 score 39 stars 10 scripts 36 exports 91 dependencies

Last updated from:9ed8b755fd. Checks:5 ERROR, 2 OK, 2 WARNING. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	327
source / vignettes	OK	419
linux-release-x86_64	ERROR	330
macos-release-arm64	WARNING	162
macos-oldrel-arm64	WARNING	146
windows-devel	ERROR	303
windows-release	ERROR	258
windows-oldrel	ERROR	240
wasm-release	OK	274

Exports:annot_data annot_data_exons annot_data_genes annot_data_transcripts annot_row_names as_isoformic col_data col_names ContextData create_context_data de_gene de_tx download_reference get_isoformic_cache is_deg_sig IsoformicExperiment join_DEG_DET make_tx_to_gene plot_genomic_context plot_log2fc plot_log2FC plot_tx_context plot_tx_expr prepare_annotation prepare_annotation_db prepare_exon_annotation prepare_isoformic_annotation prepare_profile_data row_data row_names run_enrichment salmon_index salmon_quant tx_annot tx_to_gene tx_type_palette

Dependencies:abind arrow assertthat backports bit bit64 boot broom car carData cli clipr colorspace corrplot cowplot cpp11 crayon DBI Deriv doBy dplyr duckdb farver forecast Formula fracdiff fs generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable hms isoband labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mgcv minqa modelr nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig polynom prettyunits progress purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas rlang rstatix S7 scales SparseM stringi stringr survival tibble tidyr tidyselect timeDate tzdb urca utf8 vctrs viridisLite vroom withr zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert a SummarizedExperiment to an IsoformicExperiment Object	as_isoformic
Create ContextData Object	create_context_data
Download Reference Files from GENCODE	download_reference
Retrieve System-Dependent Cache Path for Isoformic	get_isoformic_cache
Annotate Transcripts with Differential Gene Expression Significance	is_deg_sig
IsoformicExperiment Class	annot_data annot_data_exons annot_data_genes annot_data_transcripts annot_row_names col_data col_names de_gene de_tx IsoformicExperiment row_data row_names tx_annot tx_to_gene
Merge Gene and Transcript Level Differential Expression Tables	join_DEG_DET
Create Transcript-to-Gene Relationship Table	make_tx_to_gene
Plot Transcripts Genomic Context	plot_genomic_context
Plot Log2 Fold-Change Results for Transcripts of Selected Genes	plot_log2FC plot_log2fc
Plot Transcript Genomic Context	plot_tx_context
Plot Transcript per gene expression	plot_tx_expr
Prepare Annotation	prepare_annotation
Write Parquet File from GFF	prepare_annotation_db
Prepare Exon based Position Annotation Table	prepare_exon_annotation
Write Feature Annotation to Parquet Files	prepare_isoformic_annotation
Prepare Data for Gene and Transcript Expression Profile Plot	prepare_profile_data
Run Gene Set Enrichment Analysis for Different Transcript Types	run_enrichment
Build Salmon Index	salmon_index
Run Salmon Quantification	salmon_quant
Transcript Type Color Palette	tx_type_palette