Releases · dpeerlab/seqc · GitHub

26 Mar 13:17

hisplan

v0.2.11 Latest

Latest

Includes 10x-compatible count matrix in the final outputs.
Uses --force-glacier-transfer to force download operations on restored Glacier objects.

Assets 2

26 Aug 16:55

hisplan

v0.2.10

Generates a Cell Ranger compatible count matrix.
Due to the known non-platform agnostic glob behavior, it is possible that L001_R1 is merged with L002_R2 (not L001_R2). To avoid this problem, we first sort genomic_fastq and barcode_fastq before merging. This is a temporary hacky solution.

Assets 2

30 Jun 12:59

hisplan

v0.2.9

Fixed the bug that outputs slightly less number of UMI correction data. This fix should give a little better result for RNA Velocity.

Assets 2

24 Oct 16:14

hisplan

v0.2.8

Set min-poly-t to 0 for 10x v2 and 10x v3.
Should run with the new AMI that contains STAR 2.7.6a.

Assets 2

09 Oct 16:43

hisplan

v0.2.7

Increased memory requirements for RMT correction.
Uses r5.4xlarge as default instance type.
Logs the running time before uploading the log file.

Assets 2

07 Oct 23:10

hisplan

v0.2.6

SEQC run
- Refactored RMT correction module to use Dask and Numba to reduce the running time by 3-4 hours.
- Uses np.int64 to store UMI (not np.int32).
- Generates CB/UMI correction files (info needed for tagging BAM)
- Fixed the bug that incorrectly marks some cells as RMT error.
- Replaced Deprecated Pandas functions (e.g. as_matrix)
- Uses Pickle protocol=4 to serialize a byte object larger than 4 GiB
- Now requires pandas>=1.0.4, statsmodels=0.11.1, scipy>=1.5.1.
- Uses PhenoGraph 1.5.7.
- Writes software versions in the log file (SEQC, STAR, and samtools)
- Log running time.
- Terminates gracefully when running locally.
- Terminates gracefully when error occurred while running locally.
- Handles output_prefix properly.
SEQC index
- Supports --local, --emsemble-release, and --read-length.
- Handles when genome FASTA is gzipped.
- Changed the default valid biotypes to protein_coding, lincRNA, antisense, IG_V_gene, IG_D_gene, IG_J_gene, IG_C_gene, TR_V_gene, TR_D_gene, TR_J_gene, TR_C_gene.
- Preserve STAR log file (Log.out).
- Improves logging.
- Fixed to respect the --folder and --valid-biotypes argument.

Assets 2

02 Oct 21:56

hisplan

v0.2.5

To handle snRNA-seq data and maintain the backward compatibility, --filter-mode is introduced.
Allows to override --max_insert_size if the filter mode is snRNA-seq.
Sets figure facecolor to white by default in the analysis notebook template (go dark theme!)

Assets 2

19 Sep 20:33

hisplan

v0.2.4

Change the default EC2 instance type to r5.2xlarge
Update the installation steps
Fix MAGIC & PhenoGraph installation
Install MAGIC v0.1.1 and PhenoGraph v1.5.2 from the dpeerlab repository
Use magic.MAGIC_core in the notebook

Assets 2

23 Jul 18:36

hisplan

v0.2.3-alpha.5 Pre-release

Pre-release

Support 10x v3 chemistry
Add additional command-line arguments:
- --ami-id: controls which AMI to use
- --user-tags: adds custom tags to EC2 instance
- --remote-update: installs the local SEQC package onto EC2 instance
- --terminate and --no-terminate: controls whether or not EC2 instance will be terminated upon completion
Set version to v0.2.3

Assets 2

23 Jul 18:31

hisplan

v0.2.2

In-drop v5 support

Assets 2