Releases: Kuanhao-Chao/splam
Releases · Kuanhao-Chao/splam
v1.0.10
v1.0.10 (2023-11-16)
Main features
- Update Spam extraction mode to support both (1) gene - transcript - exon and (2) transcript - exon hierarchies.
- Add new test example at: https://github.com/Kuanhao-Chao/splam/blob/main/test/script_annotation_lncRNA.sh
Documentation:
The link to the documentation: http://ccb.jhu.edu/splam/
v1.0.9
v1.0.9 (2023-09-20)
Main features
- Fix the function for extracting chromosome sizes from the FASTA file
- Add two arguments for the Splam extract mode: --fr and --rf. These arguments set the strand if the alignment does not have an XS tag.
--fr
: assume stranded library fr-secondstrand--rf
: assume stranded library rf-firststrand
Documentation:
The link to the documentation: http://ccb.jhu.edu/splam/
v1.0.8
v1.0.8 (2023-09-20)
Main features
- Fix PyPi README rendering issue
Documentation:
The link to the documentation: http://ccb.jhu.edu/splam/
v1.0.3 release
v1.0.3 (2023-08-28)
Main features
- Remove
-A / --assembly-report
argument. Splam now directly reads the length of each chromosome through fasta file and can work with any assemblies.
Documentation:
The link to the documentation: http://ccb.jhu.edu/splam/
v1.0.2 initial release
v1.0.2 (2023-07-31)
This is the initial release of the Splam code and documentation.
Documentation:
The link to the documentation: http://ccb.jhu.edu/splam/
Main features
- Trained deep residual convolutional neural network Splam model - Pytorch and Torchscript
- Extracting splice junctions in alignment files or introns in annotation files
splam extract
- doc link - Scoring extracted splice junctions or introns using Splam model
splam score
- doc link - Cleaning up spurious splice junctions in alignment files
splam clean
- doc link
Scripts for model training & testing
- The scripts for Splam model training, testing, and data analysis are available at this GitHub repository
PyPi release
- Splam v1.0.2 is also available on PyPi: https://pypi.org/manage/project/splam/release/1.0.2/