# Tools to work with a Compendium of 181000 human transcriptome sequencing studies

## Documentation for package ‘HumanTranscriptomeCompendium’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

addRD | add gene-level rowData derived from transcript level rowRanges
ca43k | app to survey 43000 cancer transcriptomes
get_ds4841 | return instance of ssrch::DocSet with metadata on 4841 human transcriptome studies in NCBI SRA
htx_app | explore SRA metadata
htx_load | load a SummarizedExperiment shell for the Human Transcriptome Compendium
htx_query_by_study_accession | retrieve 'restfulSE' SummarizedExperiment instance for selected studies in htx compendium
htx_query_by_text | subset compendium through keyword lookup
HumanTranscriptomeCompendium.colnames | character vector of available samples in HDF cloud assay representation
load_bigrnaFiles | obtain listing of contents of BigRNA compendium (salmon runs)
load_experTable | obtain listing of experiments and submission date/time in compendium
load_studTable | obtain listing of all studies in compendium
path_doc4842 | return path to metadata csvs in zip file
procExpToGene | acquire a single sample from bigRNA compendium specified by accession and develop gene-level quantifications using tximport
tx2gene_gencode27 | generate a data.frame mapping gencode 27 ensembl transcript identifiers to ensembl gene identifiers
uniqueAcc_120518 | experiment accessions available in compendium as of may 12 2018