Releases: SpatialTranscriptomicsResearch/st_pipeline
Releases · SpatialTranscriptomicsResearch/st_pipeline
ST Pipeline release
ST Pipeline release
- Fixed a small bug when soring the output of taggd
- Improved the st_qa.py script
ST Pipeline release
- Removed parallel code for un-necessary parts
- Added option to provide saturation points
ST Pipeline release
- Improved the st_qa.py script
- Few small improvements in the annotation step
- Added support to use a transcriptome (--transcriptome)
ST Pipeline release
- Fixed an error in the parameters
ST Pipeline release
- Made the parsing of unique UMIs gene by gene and parallel
- AdjacentBi is now the default method for UMI counting
- Made the trimming function output the trimmed R2 in BAM format with the barcode and UMI
- Made the mapping function works with a BAM file as input (latest STAR release)
- Made the annotation function parallel
- Made the quality step parallel
- Improvements in speed and memory (constant memory use)
- The STAR genome loading strategy can be now set
- Added an affinity based method to cluster UMIs
- Added option to set the STAR BAM sort memory limit
ST Pipeline release
- Fixed a bug that would make the matrix of counts inverted
ST Pipeline Release
- st_qa.py generate expression heatmap plots
- Fixed a minor bug in the computation of the saturation curves
- adjust_matrix_coordinates now does not update the coordinates by default
- adjust_matrix_coordiantes works with the latest ST Spot detector format
- small updates in the fastq merging script
- relaxed a bit the restriction checks for some parameters
ST Pipeline release
- Added new useful scripts
- Bumped PySAM and HTSeq
ST Pipeline release
Changed the order in the requirements file to make PIP more compatible