Package: tidybulk 1.19.0
Stefano Mangiola
tidybulk: Brings transcriptomics to the tidyverse
This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.
Authors:
tidybulk_1.19.0.tar.gz
tidybulk_1.19.0.zip(r-4.5)tidybulk_1.19.0.zip(r-4.4)tidybulk_1.17.4.zip(r-4.3)
tidybulk_1.19.0.tgz(r-4.4-any)tidybulk_1.17.4.tgz(r-4.3-any)
tidybulk_1.19.0.tar.gz(r-4.5-noble)tidybulk_1.19.0.tar.gz(r-4.4-noble)
tidybulk_1.19.0.tgz(r-4.4-emscripten)tidybulk_1.17.4.tgz(r-4.3-emscripten)
tidybulk.pdf |tidybulk.html✨
tidybulk/json (API)
| # Install 'tidybulk' in R: |
| install.packages('tidybulk', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stemangiola/tidybulk/issues
- X_cibersort - Cibersort reference
- breast_tcga_mini_SE - Needed for vignette breast_tcga_mini_SE
- counts_ensembl - Counts with ensembl annotation
- ensembl_symbol_mapping - Data set
- flybaseIDs - FlybaseIDs
- se - SummarizedExperiment
- se_mini - SummarizedExperiment mini for vignette
- tximeta_summarizeToGene_object - Needed for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximeta
- vignette_manuscript_signature_boxplot - Needed for vignette vignette_manuscript_signature_boxplot
- vignette_manuscript_signature_tsne - Needed for vignette vignette_manuscript_signature_tsne
- vignette_manuscript_signature_tsne2 - Needed for vignette vignette_manuscript_signature_tsne2
On BioConductor:tidybulk-1.19.0(bioc 3.21)tidybulk-1.18.0(bioc 3.20)
assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsbioconductorbulk-transcriptional-analysesdeseq2differential-expressionedgerensembl-idsentrezgene-symbolsgseamds-dimensionspcapiperedundancytibbletidytidy-datatidyversetranscriptstsne
Last updated 2 months agofrom:1a18995d8a. Checks:OK: 1 ERROR: 3 NOTE: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | NOTE | Dec 19 2024 |
| R-4.5-linux | ERROR | Dec 19 2024 |
| R-4.4-win | NOTE | Dec 19 2024 |
| R-4.4-mac | NOTE | Dec 19 2024 |
| R-4.3-win | ERROR | Sep 24 2024 |
| R-4.3-mac | ERROR | Sep 24 2024 |
Exports:%>%adjust_abundanceaggregate_duplicatesarrangeas_matrixas_SummarizedExperimentas_tibblebind_colscluster_elementsdeconvolve_cellularitydescribe_transcriptdistinctdoensembl_to_symbolfill_missing_abundancefilterfull_joinget_bibliographygroup_byidentify_abundantimpute_missing_abundanceinner_joinkeep_abundantkeep_variableleft_joinlog10_reverse_translogit_transmutatenestpivot_samplepivot_transcriptquantile_normalise_abundancereduce_dimensionsremove_redundancyrenameresolve_complete_confounders_of_non_interestright_joinrotate_dimensionsrowwisescale_abundanceselectsummarisesymbol_to_entreztest_differential_abundancetest_differential_cellularitytest_gene_enrichmenttest_gene_overrepresentationtest_gene_ranktest_stratification_cellularitytibbletidybulktidybulk_SAM_BAMunnest
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbitbit64bslibcachemclicliprcolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypreprocessCoreprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownS4ArraysS4VectorssassscalesSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexttservicetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adjust transcript abundance for unwanted variation | adjust_abundance adjust_abundance,RangedSummarizedExperiment-method adjust_abundance,spec_tbl_df-method adjust_abundance,SummarizedExperiment-method adjust_abundance,tbl_df-method adjust_abundance,tidybulk-method |
| Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columns | aggregate_duplicates aggregate_duplicates,RangedSummarizedExperiment-method aggregate_duplicates,spec_tbl_df-method aggregate_duplicates,SummarizedExperiment-method aggregate_duplicates,tbl_df-method aggregate_duplicates,tidybulk-method |
| Arrange rows by column values | arrange |
| Get matrix from tibble | as_matrix |
| as_SummarizedExperiment | as_SummarizedExperiment as_SummarizedExperiment,spec_tbl_df-method as_SummarizedExperiment,tbl_df-method as_SummarizedExperiment,tidybulk-method |
| Left join datasets | bind_cols left_join |
| Efficiently bind multiple data frames by row and column | bind_rows |
| Needed for vignette breast_tcga_mini_SE | breast_tcga_mini_SE |
| Get clusters of elements (e.g., samples or transcripts) | cluster_elements cluster_elements,RangedSummarizedExperiment-method cluster_elements,spec_tbl_df-method cluster_elements,SummarizedExperiment-method cluster_elements,tbl_df-method cluster_elements,tidybulk-method |
| Counts with ensembl annotation | counts_ensembl |
| Get cell type proportions from samples | deconvolve_cellularity deconvolve_cellularity,RangedSummarizedExperiment-method deconvolve_cellularity,spec_tbl_df-method deconvolve_cellularity,SummarizedExperiment-method deconvolve_cellularity,tbl_df-method deconvolve_cellularity,tidybulk-method |
| Get DESCRIPTION from gene SYMBOL for Human and Mouse | .describe_transcript_SE describe_transcript describe_transcript,RangedSummarizedExperiment-method describe_transcript,spec_tbl_df-method describe_transcript,SummarizedExperiment-method describe_transcript,tbl_df-method describe_transcript,tidybulk-method |
| distinct | distinct |
| Data set | ensembl_symbol_mapping |
| Add transcript symbol column from ensembl id for human and mouse data | ensembl_to_symbol ensembl_to_symbol,spec_tbl_df-method ensembl_to_symbol,tbl_df-method ensembl_to_symbol,tidybulk-method |
| Fill transcript abundance if missing from sample-transcript pairs | fill_missing_abundance fill_missing_abundance,spec_tbl_df-method fill_missing_abundance,tbl_df-method fill_missing_abundance,tidybulk-method |
| Subset rows using column values | filter |
| flybaseIDs | flybaseIDs |
| Produces the bibliography list of your workflow | get_bibliography get_bibliography,RangedSummarizedExperiment-method get_bibliography,spec_tbl_df-method get_bibliography,SummarizedExperiment-method get_bibliography,tbl-method get_bibliography,tbl_df-method get_bibliography,tidybulk-method |
| Group by one or more variables | group_by |
| find abundant transcripts | identify_abundant identify_abundant,RangedSummarizedExperiment-method identify_abundant,spec_tbl_df-method identify_abundant,SummarizedExperiment-method identify_abundant,tbl_df-method identify_abundant,tidybulk-method |
| impute transcript abundance if missing from sample-transcript pairs | impute_missing_abundance impute_missing_abundance,RangedSummarizedExperiment-method impute_missing_abundance,spec_tbl_df-method impute_missing_abundance,SummarizedExperiment-method impute_missing_abundance,tbl_df-method impute_missing_abundance,tidybulk-method |
| Inner join datasets | full_join inner_join right_join |
| Keep abundant transcripts | keep_abundant keep_abundant,RangedSummarizedExperiment-method keep_abundant,spec_tbl_df-method keep_abundant,SummarizedExperiment-method keep_abundant,tbl_df-method keep_abundant,tidybulk-method |
| Keep variable transcripts | keep_variable keep_variable,RangedSummarizedExperiment-method keep_variable,spec_tbl_df-method keep_variable,SummarizedExperiment-method keep_variable,tbl_df-method keep_variable,tidybulk-method |
| log10_reverse_trans | log10_reverse_trans |
| logit scale | logit_trans |
| Create, modify, and delete columns | mutate |
| Extract sample-wise information | pivot_sample pivot_sample,RangedSummarizedExperiment-method pivot_sample,spec_tbl_df-method pivot_sample,SummarizedExperiment-method pivot_sample,tbl_df-method pivot_sample,tidybulk-method |
| Extract transcript-wise information | pivot_transcript pivot_transcript,RangedSummarizedExperiment-method pivot_transcript,spec_tbl_df-method pivot_transcript,SummarizedExperiment-method pivot_transcript,tbl_df-method pivot_transcript,tidybulk-method |
| Normalise by quantiles the counts of transcripts/genes | quantile_normalise_abundance quantile_normalise_abundance,RangedSummarizedExperiment-method quantile_normalise_abundance,spec_tbl_df-method quantile_normalise_abundance,SummarizedExperiment-method quantile_normalise_abundance,tbl_df-method quantile_normalise_abundance,tidybulk-method |
| Dimension reduction of the transcript abundance data | reduce_dimensions reduce_dimensions,RangedSummarizedExperiment-method reduce_dimensions,spec_tbl_df-method reduce_dimensions,SummarizedExperiment-method reduce_dimensions,tbl_df-method reduce_dimensions,tidybulk-method |
| Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) abundances are correlated | remove_redundancy remove_redundancy,RangedSummarizedExperiment-method remove_redundancy,spec_tbl_df-method remove_redundancy,SummarizedExperiment-method remove_redundancy,tbl_df-method remove_redundancy,tidybulk-method |
| Rename columns | rename |
| Resolve Complete Confounders of Non-Interest | resolve_complete_confounders_of_non_interest resolve_complete_confounders_of_non_interest,RangedSummarizedExperiment-method resolve_complete_confounders_of_non_interest,SummarizedExperiment-method |
| Rotate two dimensions (e.g., principal components) of an arbitrary angle | rotate_dimensions rotate_dimensions,RangedSummarizedExperiment-method rotate_dimensions,spec_tbl_df-method rotate_dimensions,SummarizedExperiment-method rotate_dimensions,tbl_df-method rotate_dimensions,tidybulk-method |
| Group input by rows | rowwise |
| Scale the counts of transcripts/genes | scale_abundance scale_abundance,RangedSummarizedExperiment-method scale_abundance,spec_tbl_df-method scale_abundance,SummarizedExperiment-method scale_abundance,tbl_df-method scale_abundance,tidybulk-method |
| SummarizedExperiment | se |
| SummarizedExperiment mini for vignette | se_mini |
| Summarise each group to fewer rows | summarise |
| Get ENTREZ id from gene SYMBOL | symbol_to_entrez |
| Perform differential transcription testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2 | test_differential_abundance test_differential_abundance,RangedSummarizedExperiment-method test_differential_abundance,spec_tbl_df-method test_differential_abundance,SummarizedExperiment-method test_differential_abundance,tbl_df-method test_differential_abundance,tidybulk-method |
| Add differential tissue composition information to a tbl | test_differential_cellularity test_differential_cellularity,RangedSummarizedExperiment-method test_differential_cellularity,spec_tbl_df-method test_differential_cellularity,SummarizedExperiment-method test_differential_cellularity,tbl_df-method test_differential_cellularity,tidybulk-method |
| analyse gene enrichment with EGSEA | test_gene_enrichment test_gene_enrichment,RangedSummarizedExperiment-method test_gene_enrichment,spec_tbl_df-method test_gene_enrichment,SummarizedExperiment-method test_gene_enrichment,tbl_df-method test_gene_enrichment,tidybulk-method |
| analyse gene over-representation with GSEA | test_gene_overrepresentation test_gene_overrepresentation,RangedSummarizedExperiment-method test_gene_overrepresentation,spec_tbl_df-method test_gene_overrepresentation,SummarizedExperiment-method test_gene_overrepresentation,tbl_df-method test_gene_overrepresentation,tidybulk-method |
| analyse gene rank with GSEA | test_gene_rank test_gene_rank,RangedSummarizedExperiment-method test_gene_rank,spec_tbl_df-method test_gene_rank,SummarizedExperiment-method test_gene_rank,tbl_df-method test_gene_rank,tidybulk-method |
| Test of stratification of biological replicates based on tissue composition, one cell-type at the time, using Kaplan-meier curves. | test_stratification_cellularity test_stratification_cellularity,RangedSummarizedExperiment-method test_stratification_cellularity,spec_tbl_df-method test_stratification_cellularity,SummarizedExperiment-method test_stratification_cellularity,tbl_df-method test_stratification_cellularity,tidybulk-method |
| Creates an annotated `tidybulk` tibble from a `tbl` or `SummarizedExperiment` object | tidybulk tidybulk,RangedSummarizedExperiment-method tidybulk,spec_tbl_df-method tidybulk,SummarizedExperiment-method tidybulk,tbl_df-method |
| Creates a `tt` object from a list of file names of BAM/SAM | tidybulk_SAM_BAM tidybulk_SAM_BAM,character,character-method |
| Needed for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximeta | tximeta_summarizeToGene_object |
| unnest | nest unnest |
| Needed for vignette vignette_manuscript_signature_boxplot | vignette_manuscript_signature_boxplot |
| Needed for vignette vignette_manuscript_signature_tsne | vignette_manuscript_signature_tsne |
| Needed for vignette vignette_manuscript_signature_tsne2 | vignette_manuscript_signature_tsne2 |
| Cibersort reference | X_cibersort |
