History

Development on GitHub

  • fix bug with GT_tag2 in match_VCF_samples() function

Release v0.5.8 (18/02/2023)

  • fix issue with None in match() and match_SNPs() when w/ chr w/o chr have partial match

  • minor optimise the codes for vireoSNP.utils.vcf_utils.parse_donor_GPb

  • add a snp_gene_match() function

  • fix issue in write_VCF() when there is no samples

Release v0.5.7 (24/03/2022)

  • fix the issue when output_dir is not given

  • add doc for read VCF files

Release v0.5.6 (07/04/2021)

  • fix a bug for detecting unsupported genotyep tag

  • add a wrap function to compare samples in two VCF files

  • add doublet_logLikRatio in donor_ids.tsv for extra indicators of doublets

  • update documentation with supporting notebook vireoSNP_clones.ipynb

  • update API

Release v0.5.5 (28/03/2021)

  • update notebook vireoSNP_clones.ipynb

  • update API

Release v0.5.4 (28/03/2021)

  • introduce log likelihood ratio for detecting ambient RNAs

  • support ambient RNAs from a mixture of all donors or only two donors

  • introduce multiple processes for multiple initializations

  • introduce ELBO_gain for selecting variants

  • For donor_ids.tsv, the doublet_prob change from sum to max

Release v0.5.3 (28/03/2021)

  • support detection of ambient RNAs, alternative way for doublet detection

Release v0.5.0 (09/02/2021)

  • support support numpy.ndarray and automatically change to sparse matrix

  • fix the sign of KL

  • fix a minor bug on –noDoublet setting

  • add –cellRange to subset the input cells for less memory

  • update anno_heat() plotting

  • add get_confusion() for results comparison and plotting

Release v0.4.2 (14/11/2020)

  • fix the donor names when N < donors_in_GT

  • change the suggestion from cellSNP python to C version (cellsnp-lite)

Release v0.4.1 (18/05/2020)

  • add likelihood ratio test the differential donor abundance in bulk RNA-seq data

  • set the interpolation=’none’ for plt.imshow

Release v0.4.0 (19/04/2020)

  • add vireoBulk for demultiplexing in bulk RNA-seq data

Release v0.3.2 (10/04/2020)

  • support donor variant match between with and without “chr” prefix

Release v0.3.1 (25/03/2020)

  • replace greed_match to optimal_match for aligning donors via genotype

Release v0.3.0 (23/03/2020)

  • Rewrite the Vireo in the object-oriented way for easier upgrading and adding new features

  • Now support fix the dispersion of the theta posterior distribution

  • Change delay_fit_theta as an augument. It’s often useful for donor deconvolution, but may not ideal for clonal inference, where theta can be very different from our expectation due to ASE or copy numbers

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