NEWS.md

In LiNk-NY/TENxIO: Import methods for 10X Genomics files

Changes in version 1.8.0

New features

• The import method for h5 files now includes all rowData which typically includes "ID", "Symbol", and "Type" columns.

Bug fixes and minor improvements

• rownames are set to first column in the features.tsv.gz data (rownames for h5 files are determined by HDF5Array::TENxMatrix)
• TENxH5 now tests whether there is a /matrix/features/interval dataset in the h5 file. It sets ranges to NA_character_ when interval data is not found.

Changes in version 1.6.0

Bug fixes and minor improvements

• Use rowData from filtered SingleCellExperiment object (@MalteThodberg, #5)
• Add examples to TENxFileList documentation and improve constructor function

Changes in version 1.4.0

Bug fixes and minor improvements

• Skip unit tests when remote H5 access is not configured.

Changes in version 1.2.0

New features

• TENxTSV class has been added to handle compressed and uncompressed TSV files.

Bug fixes and minor improvements

• The import method for TENxFileList was returning a nested SummarizedExperiment within the SingleCellExperiment. The counts and assay(..., i="counts") methods should only return the bare Matrix rather than the embedded SummarizedExperiment (@dgastn, #2).

Changes in version 1.0.0

• Package released in Bioconductor!

LiNk-NY/TENxIO documentation built on Dec. 6, 2024, 8:38 a.m.