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Release Note

v0.5.3

2018-05-10

2be1954

Features

  • Plot demultiplexing and alignment stats to help users assess their data.
  • Column names of UMI-count matrix is named in a format of 'BC-i-xxxx' to suit users needs.

v0.5.2

2018-04-16

Features

  • Generate QC plots for UMI-counts matrices. If ST is performed, an extra QC plot masked on grid is generated.
  • Allow experienced users to feed extra parameters to align. See issue #10.

v0.5.1

2018-04-05

Features

  • Get rid of the possible limitation about "shared memory" when STAR is used on servers.
  • SpatialTranscriptomics (ST) processing is able to use STAR aligner practically.
  • Optionally remove intermediate files in a robust way.

v0.4.8

2018-03-26

Features

  • Robust selection on type of genes, e.g., protein coding, lincRNA.
    • Handle the case when all genes are needed.
    • The gene names are consistent to the in-house inDrop pipeline using genometools.
    • Handle the GTF/GFF where "gene_biotype" attribute is not available.
  • Automatically remove intermediate files by snakemake's temp() function.

v0.4.7

2018-03-23

Features

  • Support "gene_biotype" selection.
  • Better support SpatialTranscriptome data.
    • celseq2-to-st understands expr.csv file
    • celseq2-to-st recognizes "(1 out of many)" annotation inside GTF/GFF.
  • Robust design of work flow.

v0.4.4

2018-02-13

Features

  • Improve the design of snakemake pipeline to avoid silent pre-inhibition.
  • Improve running with STAR to avoid memory over-use.

v0.4.1

2017-12-20

Features

  • Support STAR aligner.
  • Update docs.

v0.4.0

2017-10-04

Features

  • More general API to specify UMI-BC design.
  • Support st_pipeline.

v0.3.0

2017-09-18

Features

  • Simulate CEL-Seq2 reads.
  • 🔫 Release package tests.

v0.2.6

2017-09-14

Features

  • Support "reverse" stranded by addingstranded parameter.

v0.2.5

2017-08-22

Features

  • Add celseq2-slim to do storage management.

v0.2.0

2017-08-12

Features

  • Release command to generate templates to keep consistency.