NEWS

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ribiosIO 1.1.0 (2026-02-20)

• Initial CRAN submission
• Package prepared for CRAN submission with comprehensive documentation
• Depends on ribiosUtils (on CRAN)

ribiosIO 1.0.43

• loadObject allows the obj option to take the value NULL

ribiosIO 1.0.42

• Improve read_gct.c by providing meaningful error messages when file is inconsistent

ribiosIO 1.0.41

• read_rocheNGS_exprs renamed to read_biokit_exprs
• read_biokit_exprs updated for new Biokit pipeline output files
• Add read_trimmed_lines
• Add loadObject

ribiosIO 1.0.36

• read_rocheNGS_exprs: skip the header line

ribiosIO 1.0.35

• readMatrix added option 'as.matrix'

ribiosIO 1.0.34

• Add parameter to control NA format in write_gct

ribiosIO 1.0.32

• Start using roxygen2
• Add writeMatrix and readMatrix for numerical matrix I/O

ribiosIO 1.0.31

• writeList renamed to write.tableList
• C-level functions renamed to avoid confusion with R function names

ribiosIO 1.0.30

• Add writeList function to write a series of tables

ribiosIO 1.0.28

• read_gmt_list uses gene-set names as names of the returning list

ribiosIO 1.0.27

• write_gmt supports simple lists as input

ribiosIO 1.0.26

• read_gct_matrix prints detailed error messages for column mismatches

ribiosIO 1.0.25

• Add function read_pheno to import pheno data information

ribiosIO 1.0.24

• Bug fix: read_gmt_list supports gene sets without any genes

ribiosIO 1.0.23

• Bug fixes for read_exprs_matrix
• read_exprs_matrix reads in description of gct files

ribiosIO 1.0.22

• write_gct handles 0-row matrix

ribiosIO 1.0.21

• read_exprs_matrix handles non-numeric second column

ribiosIO 1.0.20

• Add new function read_chip to read chip files

ribiosIO 1.0.19

• Add new function write_gmt_list to export GMT lists

ribiosIO 1.0.18

• Add read_cls for reading CLS files

ribiosIO 1.0.17

• write_gct uses the 'desc' attribute of input matrix if available

ribiosIO 1.0.16

• read_exprs_matrix uses more stringent grep to detect GCT files

ribiosIO 1.0.15

• Add write_gct function to export Matrix in GCT format
• read_exprs_matrix does not interpret hashes as comment char

ribiosIO 1.0.14

• read_gct C file: second line less strict, allowing empty cells

ribiosIO 1.0.13

• isGctFile is less strict regarding spaces

ribiosIO 1.0.12

• Add isGctFile function to determine GCT file format compliance

ribiosIO 1.0.11

• Documentation improvements for read_gmt_list

ribiosIO 1.0.10

• Cleanup src/Makevar: remove hard-coded dependencies

ribiosIO 1.0.9

• Add read_fasta and write_fasta for FASTA-format sequence files

ribiosIO 1.0.8

• C-function read_gct supports both file and character string input
• Add read_gctstr_matrix for parsing GCT format strings

ribiosIO 1.0.7

• Add loadFile from the ribios package

ribiosIO 1.0.6

• Package cleanup and benchmarking

ribiosIO 1.0.5

• Add man pages for read_gmt_list and iofile

ribiosIO 1.0.4

• Add read_gmt_list function to read GMT files

ribiosIO 1.0.3

• Add correct version of iofile

ribiosIO 1.0.2

• read_exprs_matrix supports full table and duplicated row names

ribiosIO 1.0.1

• Add read_exprs_matrix for importing expression matrix from file
• C routine read_gct checks second line with arrayMax

ribiosIO 1.0.0

• Initial release: refactor read_gct from ribiosExpression