Man pages for stemangiola/ttBulk
Friendly tidy wrappers for facilitating transcriptional analyses

add_adjusted_counts_for_unwanted_variation_bulkAdd adjusted count for some batch effect
add_attrAdd attribute to abject
add_cell_type_proportionsAdd cell type proportions from cibersort
add_classAdd class to abject
add_clusters_kmeans_bulkAdd K-mean clusters to a tibble
add_clusters_SNN_bulkAdd SNN shared nearest neighbour clusters to a tibble
add_differential_transcript_abundance_bulkAdd differential transcription information to a tibble using...
add_normalised_counts_bulkAdd a tibble with normalised counts using TMM
add_normalised_counts_bulk.calcNormFactorCalculate the norm factor with calcNormFactor from limma
add_normalised_counts_bulk.get_cpmGet count per million for TMM normalisation.
add_normalised_counts_bulk.get_low_expressedDrop lowly tanscribed genes for TMM normalization
add_reduced_dimensions_MDS_bulkAdd dimensionality information to a tibble using MDS
add_reduced_dimensions_PCA_bulkAdd principal component information to a tibble using PCA
add_reduced_dimensions_TSNE_bulkAdd principal component information to a tibble using tSNE
add_rotated_dimensionsAdd Rotated dimensions of two principal components or MDS...
add_symbol_from_ensemblAdd transcript column from ensembl gene id
adjust_abundanceAdjust transcript abundance for unwanted variation
aggregate_duplicated_transcripts_bulkAggregates multiple counts from the same samples (e.g., from...
aggregate_duplicatesAggregates multiple counts from the same samples (e.g., from...
annotate_symbolAdd transcript symbol column from ensembl id
as_matrixGet matrix from tibble
bind_rowsJoin datasets
breast_tcga_miniData set
cluster_elementsGet clusters of elements (e.g., samples or transcripts)
countsExample data set
counts_ensemblCounts with ensembl annotation
counts_miniExample data set reduced
create_tt_from_bam_sam_bulkConvert bam/sam files to a tidy gene transcript counts data...
create_tt_from_tibble_bulkCreate tt object from tibble
deconvolve_cellularityGet cell type proportions from samples
drop_classRemove class to abject
ensembl_symbol_mappingData set
error_if_counts_is_naCheck whether there are NA counts
error_if_duplicated_genesCheck whether there are duplicated genes/transcripts
error_if_log_transformedCheck whether a numeric vector has been log transformed
error_if_wrong_inputCheck whether there are NA counts
filter_variable_transcriptsIdentify variable genes for dimensionality reduction
get_abundance_norm_if_existsGet column names either from user or from attributes
get_adjusted_counts_for_unwanted_variation_bulkGet adjusted count for some batch effect
get_cell_type_proportionsGet cell type proportions from cibersort
get_clusters_kmeans_bulkGet K-mean clusters to a tibble
get_clusters_SNN_bulkGet SNN shared nearest neighbour clusters to a tibble
get_differential_transcript_abundance_bulkGet differential transcription information to a tibble using...
get_elementsGet column names either from user or from attributes
get_elements_featuresGet column names either from user or from attributes
get_elements_features_abundanceGet column names either from user or from attributes
get_normalised_counts_bulkGet a tibble with normalised counts using TMM
get_reduced_dimensions_MDS_bulkGet dimensionality information to a tibble using MDS
get_reduced_dimensions_PCA_bulkGet principal component information to a tibble using PCA
get_reduced_dimensions_TSNE_bulkGet principal component information to a tibble using tSNE
get_rotated_dimensionsGet rotated dimensions of two principal components or MDS...
get_sample_transcriptGet column names either from user or from attributes
get_sample_transcript_countsGet column names either from user or from attributes
get_symbol_from_ensembl#' after wget, this function merges hg37 and hg38 mapping...
ifelse2_pipeThis is a generalisation of ifelse that acceots an object and...
ifelse_pipeThis is a generalisation of ifelse that acceots an object and...
left_joinJoin datasets
merged_ttBulk_objectAdd cell type information on single cells
mutateMutate datasets
parse_formula.formula parser
prependFrom rlang deprecated
reduce_dimensionsDimension reduction of the transcript abundance data
remove_redundancyDrop redundant elements (e.g., samples) for which feature...
remove_redundancy_elements_though_reduced_dimensionsIdentifies the closest pairs in a MDS contaxt and return one...
remove_redundancy_elements_through_correlationDrop redundant elements (e.g., samples) for which feature...
rotate_dimensionsRotate two dimensions (e.g., principal components) of an...
scale_abundanceNormalise the counts of transcripts/genes
scale_designScale design matrix
select_closest_pairsSub function of...
test_differential_abundanceAdd differential transcription information to a tbl using...
ttBulkCreates a 'tt' object from a 'tbl"
X_cibersortCibersort reference
stemangiola/ttBulk documentation built on Dec. 8, 2019, 4:27 p.m.