v0.2.1

count

• -o is now optional. Defaults to current directory.

Documentation

• Developer docs hosted on Read the Docs.

v0.2.0

Official PyPi release.

v0.1.4

count

• New --filter option. This option generates a filtered count matrix. It can not be used with --lamanno. Currently, this option only supports filtering with bustools.

v0.1.3

Fix for python 3.6

v0.1.2

info

• Updated information (now includes examples and citations)

v0.1.1

kb

• New --list option to display supported single-cell technologies
• Updated help messages and print statements overall

ref

• Can download prebuilt indices (but not for --lamanno)

count

• Support for --loom and --h5ad with --lamanno

v0.0.8

info

• Displays current package, kallisto and bustools versions.

ref

• Input arguments have changed: ref now takes a genomic FASTA file and GTF as positional arguments
• The genome is sliced into cDNA and intron (if --velocity) FASTAs
• New option: -c Path to the cDNA FASTA to be generated
• New option: -n Path to the intron FASTA to be generated (required for --velocity)
• New option: -a Path to generate cDNA transcripts to be captured (required for --velocity)
• New option: -r Path to generate intron transcripts to be captured (required for --velocity)

Binaries

• Kallisto and Bustools binaries for Windows, Linux and MacOS are now included in the package. Run kb info for versions.

v0.0.7

ref

• New options: --velocity, -c, -n
• Implemented reference preparation for RNA velocity. -c and -n must be provided.

v0.0.5

count

• Now runs bustools inspect and outputs the results to inspect.json file within the output directory.

v0.0.4

count

• Convert count matrices into loom files with --loom option
• Convert count matrices into h5ad files with --h5ad option