History
Release v0.2.3 (22/03/2020)
- Fix a minor bug in donor_select()
Release v0.2.2 (21/03/2020)
- Change GP_prob’s shape from (n_var, n_GT, n_donor) to (n_var, n_donor, n_GT)
- Restructure the codes for further upgrading
- Minor fix the GT_plot xlim and ylim
Release v0.2.1 (30/01/2020)
- Fix a bug when the donors in the input GT is smaller than donors in the pooled
scRNA-seq. The sample id is now corrected.
Release v0.2.0 (28/01/2020)
- Support SNP specific allelic ratio, namely theta parameters. Note, SNP based
ASE mode requires a much stronger prior on theta to avoid overfitting, as each
variant has very low number of reads.
- Change the default extraDonor to 0.
- Provide examples/vireoSNP_usage.ipynb for using vireoSNP as a Python module
for general cell clustering based on allelic ratio.
Release v0.1.8 (29/10/2019)
- Further fix the bug when variants in donor genotype are not in cell vcf file
Release v0.1.7 (05/10/2019)
- Support donor genotype vcf file with different FORMAT for different variants
Release v0.1.6 (05/10/2019)
- Fix a bug when variants in donor genotype are not in cell vcf file
Release v0.1.5 (28/09/2019)
- Support genotype barcode generation
Release v0.1.4 (22/09/2019)
- Support that the case that input GT is larger than wanted n_donor
- Clarify the structure in vireo_flock: 1) warm-up for multiple initials or
extra donors; 2) pre-step to subset or fill up the genotype prior; 3) the main
run.
- Provide more options in the warm-up step to search donors from extra clusters.
Before, it only uses the size of the donor. Now, the genotype distance can be
used to search the K donors with furthest genotype distance.
Release v0.1.3 (30/08/2019)
- Support vartrix sparse matrices as input
- Change –amplifyK to –extraDonor for extra donors in initial search
- Fixed the bug for –noDoublet
- Fixed a bug for unassigned
- Minor update of figure output
- Updated the submoduals for easier import
Release v0.1.2 (15/07/2019)
- Support sparse matrices as input (for cellSNP directory with -O)
- Plot the distance between genotype probability between estimated samples
- Upgrade the manual, including the usage of simulation (readme in the
simulation folder of GitHub repo)
Release v0.1.1 (30/06/2019)
- A completed version for all planned features
- Donor deconvolution with supporting multiple modes:
1) without genotype
2) with genotype for all samples
3) with genotype for part of the samples
4) with genotype but not confident
- Manual for installation, usage, and preprocessing
- Release test data sets
- vireoSNP is available on PyPI, try it pip install vireoSNP
Release v0.1.0 (24/06/2019)
- reimplementation of vireo in Python (orignal in cardelino R package)
- Initial release with limited features