Brings transcriptomics to the tidyverse

[Up] [Top]

Documentation for package ‘tidybulk’ version 1.20.0

Help Pages

.describe_transcript_SE Get DESCRIPTION from gene SYMBOL for Human and Mouse
adjust_abundance Adjust transcript abundance for unwanted variation
adjust_abundance-method Adjust transcript abundance for unwanted variation
aggregate_duplicates Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columns
aggregate_duplicates-method Aggregates multiple counts from the same samples (e.g., from isoforms), concatenates other character columns, and averages other numeric columns
arrange Arrange rows by column values
as_matrix Get matrix from tibble
as_SummarizedExperiment as_SummarizedExperiment
as_SummarizedExperiment-method as_SummarizedExperiment
bind_cols Left join datasets
bind_rows Efficiently bind multiple data frames by row and column
breast_tcga_mini_SE Needed for vignette breast_tcga_mini_SE
cluster_elements Get clusters of elements (e.g., samples or transcripts)
cluster_elements-method Get clusters of elements (e.g., samples or transcripts)
counts_ensembl Counts with ensembl annotation
deconvolve_cellularity Get cell type proportions from samples
deconvolve_cellularity-method Get cell type proportions from samples
describe_transcript Get DESCRIPTION from gene SYMBOL for Human and Mouse
describe_transcript-method Get DESCRIPTION from gene SYMBOL for Human and Mouse
distinct distinct
ensembl_symbol_mapping Data set
ensembl_to_symbol Add transcript symbol column from ensembl id for human and mouse data
ensembl_to_symbol-method Add transcript symbol column from ensembl id for human and mouse data
fill_missing_abundance Fill transcript abundance if missing from sample-transcript pairs
fill_missing_abundance-method Fill transcript abundance if missing from sample-transcript pairs
filter Subset rows using column values
flybaseIDs flybaseIDs
full_join Inner join datasets
get_bibliography Produces the bibliography list of your workflow
get_bibliography-method Produces the bibliography list of your workflow
group_by Group by one or more variables
identify_abundant Identify abundant transcripts/genes
identify_abundant-method Identify abundant transcripts/genes
impute_missing_abundance impute transcript abundance if missing from sample-transcript pairs
impute_missing_abundance-method impute transcript abundance if missing from sample-transcript pairs
inner_join Inner join datasets
keep_abundant Filter to keep only abundant transcripts/genes
keep_abundant-method Filter to keep only abundant transcripts/genes
keep_variable Keep variable transcripts
keep_variable-method Keep variable transcripts
left_join Left join datasets
log10_reverse_trans log10_reverse_trans
logit_trans logit scale
mutate Create, modify, and delete columns
nest unnest
pivot_sample Extract sample-wise information
pivot_sample-method Extract sample-wise information
pivot_transcript Extract transcript-wise information
pivot_transcript-method Extract transcript-wise information
quantile_normalise_abundance Normalise by quantiles the counts of transcripts/genes
quantile_normalise_abundance-method Normalise by quantiles the counts of transcripts/genes
reduce_dimensions Dimension reduction of the transcript abundance data
reduce_dimensions-method Dimension reduction of the transcript abundance data
remove_redundancy Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) abundances are correlated
remove_redundancy-method Drop redundant elements (e.g., samples) for which feature (e.g., transcript/gene) abundances are correlated
rename Rename columns
resolve_complete_confounders_of_non_interest Resolve Complete Confounders of Non-Interest
resolve_complete_confounders_of_non_interest-method resolve_complete_confounders_of_non_interest
right_join Inner join datasets
rotate_dimensions Rotate two dimensions (e.g., principal components) of an arbitrary angle
rotate_dimensions-method Rotate two dimensions (e.g., principal components) of an arbitrary angle
rowwise Group input by rows
scale_abundance Scale the counts of transcripts/genes
scale_abundance-method Scale the counts of transcripts/genes
se SummarizedExperiment
se_mini SummarizedExperiment mini for vignette
summarise Summarise each group to fewer rows
symbol_to_entrez Get ENTREZ id from gene SYMBOL
test_differential_abundance 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-method Perform differential transcription testing using edgeR quasi-likelihood (QLT), edgeR likelihood-ratio (LR), limma-voom, limma-voom-with-quality-weights or DESeq2
test_differential_cellularity Add differential tissue composition information to a tbl
test_differential_cellularity-method Add differential tissue composition information to a tbl
test_gene_enrichment analyse gene enrichment with EGSEA
test_gene_enrichment-method analyse gene enrichment with EGSEA
test_gene_overrepresentation analyse gene over-representation with GSEA
test_gene_overrepresentation-method analyse gene over-representation with GSEA
test_gene_rank analyse gene rank with GSEA
test_gene_rank-method analyse gene rank with GSEA
test_stratification_cellularity Test of stratification of biological replicates based on tissue composition, one cell-type at the time, using Kaplan-meier curves.
test_stratification_cellularity-method Test of stratification of biological replicates based on tissue composition, one cell-type at the time, using Kaplan-meier curves.
tidybulk Creates an annotated 'tidybulk' tibble from a 'tbl' or 'SummarizedExperiment' object
tidybulk-method Creates an annotated 'tidybulk' tibble from a 'tbl' or 'SummarizedExperiment' object
tidybulk_SAM_BAM Creates a 'tt' object from a list of file names of BAM/SAM
tidybulk_SAM_BAM-method Creates a 'tt' object from a list of file names of BAM/SAM
tximeta_summarizeToGene_object Needed for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximeta
unnest unnest
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
X_cibersort Cibersort reference