v0.24.4

--info

• Fix typo with indropsv3

ref

• If any input (FASTA or GTF) files are provided as gzip files, they are uncompressed to the temporary directory, instead of being streamed directly. This is because ref relies on being able to access arbitrary locations of the files quickly. Working with decompressed files results in a considerable speedup.

count

• For --lamanno: spliced and unspliced busfiles no longer contain the .s suffix. This was done to make the output consistent with the normal (non--lamanno) command
• Implemented --filter with --lamanno
• Support for single nuclei RNA-seq with --nuclei. The only difference between --nuclei and --lamanno is how the spliced and unspliced matrices are combined. Specifically, --nuclei sums the matrices. Using --nuclei with neither --loom nor --h5ad results in behavior identical with --lamanno.

v0.24.3

kallisto

• Update to 0.46.1.

--info

• Updated information on indrop versions

v0.24.2

count

• fix bug with --filter where it would produce the same matrix as unfiltered

v0.24.1

ref

• kb now provides a pre-built human index for RNA velocity (linnarsson)
• The intronic fasta with the --lamanno option now includes 30-base flanking regions.

count

• Unfiltered count matrices will always be placed in the counts_unfiltered folder.
• If the --filter option is specified, the filtered count matrices will be placed in the counts_filtered folder.

v0.24.0

Official release.

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)