Package: ribiosIO 1.1.0

Jitao David Zhang

ribiosIO: Input/Output Utilities of the 'ribios' Suite

Provides data structures and functions for file input/output in the 'ribios' software suite, supporting common bioinformatics and computational biology file formats, designed for fast loading and high performance with minimal dependencies.

Authors:Jitao David Zhang [aut, cre, ctb], Balazs Banfai [ctb], F.Hoffmann-La Roche AG [cph]

ribiosIO_1.1.0.tar.gz
ribiosIO_1.1.0.zip(r-4.7)ribiosIO_1.1.0.zip(r-4.6)ribiosIO_1.1.0.zip(r-4.5)
ribiosIO_1.1.0.tgz(r-4.6-x86_64)ribiosIO_1.1.0.tgz(r-4.6-arm64)ribiosIO_1.1.0.tgz(r-4.5-x86_64)ribiosIO_1.1.0.tgz(r-4.5-arm64)
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manual.pdf |manual.html✨
card.svg |card.png
ribiosIO/json (API)
NEWS

# Install 'ribiosIO' in R:
install.packages('ribiosIO', repos = c('https://bedapub.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bedapub/ribiosio/issues

On CRAN:

Conda:

4.95 score 3 packages 33 scripts 142 downloads 50 exports 1 dependencies

Last updated from:9cfe75462c. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK109
linux-devel-x86_64OK106
source / vignettesOK165
linux-release-arm64OK103
linux-release-x86_64OK105
macos-release-arm64OK123
macos-release-x86_64OK336
macos-oldrel-arm64OK148
macos-oldrel-x86_64OK436
windows-develOK98
windows-releaseOK71
windows-oldrelOK79
wasm-releaseFAIL93

Exports:cbindGctfind_ampliseqfind_and_read_ampliseqgctDescGctMatrixgctMatrix2longdfgetDataDiriofileis_cls_fileis_factor_fileisGctFileloadFileloadObjectloadObjectInEnvloadRDSlongdf2gctMatrixread_ampliseqread_ampliseq_bedcovgctread_annotated_ampliseq_ampliconsread_bedread_biokit_exprsread_chipread_clsread_davidread_exprs_matrixread_factorread_fastaread_gct_matrixread_gctstr_matrixread_gmt_dataframeread_gmt_listread_illumina_sampleSheetread_phenoread_pheno_factorread_raw_ampliseq_ampliconsread_trimmed_linesreadMatrixreadTablesetDataDirstrList2DataFramewrite_annotated_ampliseq_ampliconswrite_clswrite_factorwrite_fastawrite_gctwrite_gmtwrite.tableListwriteMatrixwriteMatrix.tableListwriteStrList

Dependencies:ribiosUtils

Readme and manuals

Help Manual

Help pageTopics
Subsetting for GctMatrix[.GctMatrix
Transform a data.frame to a numeric matrix without characters coereced as factorsas_numeric_matrix
Coerce a GctMatrix object into a matrixas.matrix.GctMatrix
Column bind (cbind) two GctMatrix objectscbindGct
Find and read-in AmpliSeq filesfind_ampliseq find_and_read_ampliseq read_ampliseq
Retrieve feature (row) descriptions from a GctMatrix S3-objectgctDesc
Create a GctMatrix objectGctMatrix
Convert a GctMatrix into a long data framegctMatrix2longdf
Get the data directorygetDataDir
Get file names for data import/exportiofile
Check if a file encodes a factoris_cls_file is_factor_file
Test a file is a GCT file or notisGctFile
Attempt to load a binary RData fileloadFile
Load an object by its name from a RData fileloadObject
Load objects from a RData file and return them in an environmentloadObjectInEnv
Load an object from a RDS file and returns a logical flagloadRDS
Convert a long data.frame into a GctMatrixlongdf2gctMatrix
Supress warning optionallyoptional_suppress_warning
Print method for GctMatrix objectprint.GctMatrix
Read bedcov output of AmpliSeq amplicons and convert them to read countsread_ampliseq_bedcovgct
Read AmpliSeq amplicon informaiton from an annotated BED fileread_annotated_ampliseq_amplicons
Read a BED fileread_bed
qRead BioKit expression file into a data.frameread_biokit_exprs
Read CHIP fileread_chip
Read tab-delimited result files from DAVID Bioinformatics Resourcesread_david
Read an expression matrix from fileread_exprs_matrix
Read in a factor writtin in the CLS formatread_cls read_factor
Read (write) FASTA sequences into (from) named character vectorsread_fasta write_fasta
Calling C routine to read GCT file into a matrixread_gct read_gctstr_matrix read_gct_matrix
Read gene-sets in a GMT file into a data.frameread_gmt_dataframe
Calling C routine to read GMT file into a listread_gmt read_gmt_list
Read the Data block of Illumina sample sheet as data.frameread_illumina_sampleSheet
Read pheno data from CLS or tab-delimited fileread_pheno read_pheno_factor
Read AmpliSeq amplicon informaiton from an raw BED fileread_raw_ampliseq_amplicons
Read lines, thereby trimming empty spaces around the strings and removing empty linesread_trimmed_lines
Read in numeric matrix from tab-delimited format written by 'writeMatrix'readMatrix
Read in data.frame from tab-delimited format written by 'writeMatrix'readTable
Set the data directorysetDataDir
Format a string list into a data.framestrList2DataFrame
Write AmpliSeq amplicon informaiton into an annotated BED filewrite_annotated_ampliseq_amplicons
Write a factor in the CLS formatwrite_cls write_factor
Write matrix in GCT file formatwrite_gct
Write a list of gene sets into a GMT filewrite_gmt
Write a list of data.frames (tables) into fileswrite.tableList
Export matrix into a commonly used tab-delimited format inside Roche BioinformaticswriteMatrix
Write a list of data.frames (tables) into file with writeMatrixwriteMatrix.tableList
Write a list of strings in a tab-delimited filewriteStrList