scsplit - v1.0.9

Code corrected due to the deprecation of np.matrix().

- Python
Published by jon-xu over 3 years ago

scsplit - v1.0.8

Save memory space for the count matrices

- Python
Published by jon-xu over 5 years ago

scsplit - v1.0.7

Quick bug fix in generating count matrices

- Python
Published by jon-xu over 6 years ago

scsplit - v1.0.6

User control of output directory in scSplit count

- Python
Published by jon-xu over 6 years ago

scsplit - v1.0.5

allow user control of output directory

- Python
Published by jon-xu over 6 years ago

scsplit - v1.0.4

Model refining on P(S) and model likelihood Log enhancement

- Python
Published by jon-xu over 6 years ago

scsplit - v1.0.3

Bug fix for generating sample genotypes after demultiplexing.

- Python
Published by jon-xu over 6 years ago

scsplit - v1.0.2

Bug fix for the calculation of model overall likelihood Bug fix for identifying distinguishing variants when doublets are not expected

- Python
Published by jon-xu over 6 years ago

scsplit - v1.0.1

extend the support of different genotype fields in VCF (e.g. PL from GATK)

- Python
Published by jon-xu over 6 years ago

scsplit - v1.0.0

Official release

- Python
Published by jon-xu almost 7 years ago

scsplit - v0.8.5

Bug fix for demultiplexing unbalanced populations

- Python
Published by jon-xu almost 7 years ago

scsplit - v0.8.4

Allow user specify barcode tag when generating allele count matrices (default: "CB")

- Python
Published by jon-xu almost 7 years ago

scsplit - v0.8.3

enable demultiplexing 10+ mixed samples

- Python
Published by jon-xu almost 7 years ago

scsplit - v0.8.2

new function (beta) to allow demultiplexing unknown number of samples pickle dump of whole final model removed output format change for scSplitdistmatrix.csv and scSplitPAmatrix.csv output format change for scSplit_result.csv: “DBL” -> “DBL-”

- Python
Published by jon-xu almost 7 years ago

scsplit - v0.8.1

added common SNVs filtering as part of the scSplit count function with -c/--com parameter all cell assignments put in one file doublet expectation added to allow user to increase doublets based on expectation

- Python
Published by jon-xu almost 7 years ago

scsplit - v0.7.5

re-package the scripts into:

scSplit count (previous matrices.py) scSplit run (previous main.py) scSplit genotype (previous genotype.py)

- Python
Published by jon-xu about 7 years ago

scsplit - v0.6.0

Bug fixings - "ValueError: setting an array element with a sequence" when generating distinguishing variants New function - output the whole Presence/Absence Matrix for alternative alleles for all variants

- Python
Published by jon-xu about 7 years ago

scsplit - v0.5.0

enabled user-specified doublet proportion bugs fixed

- Python
Published by jon-xu about 7 years ago

scsplit - v0.4.0

• doublet detection improved
• LL calculation improved

- Python
Published by jon-xu over 7 years ago

scsplit - v0.3.0

changed PA matrix to RR/AA matrix bug fixing - distinguishing variants detection in cases where not enough can be found for the whole matrix

- Python
Published by jon-xu over 7 years ago

scsplit - v0.2.0

Important bug fixing: fixed PCA n_component in previous release caused runtime error.

- Python
Published by jon-xu over 7 years ago

scsplit - v0.1.0

A few functional updates are included in this release:

main.py: former scsplitmain.py, new functions added to detect distinguishing alleles after samples are split, so that people can use them as a reference to get samples identified; command line arguments allowed matrices.py: former scsplitmatrices.py, command line arguments allowed genotype.py: former scsplitvcf.py, command line arguments allowed simulation.py: former scsplitsimu.py, command line arguments allowed validate.py: newly added, users can use this to validate the genotypes based on the scSplit result compared to known vcf

- Python
Published by jon-xu over 7 years ago

scsplit - v0.pre

This is the first release of scSplit as a genotype-free tool for demultiplexing pooled single cell samples.

This version of scSplit toolset contains below script:

scsplitmatrices.py: build SNV x barcode Matrices (reference and alternative alleles) scsplitmain.py: main script to conduct reference free AF-based demultiplexing scsplitvcf.py: generate vcf file containing simulated genotypes according to demultiplexing assignments scsplitsimu.py: simulate BAM and allele fraction matrices based on provided vcf and BAM reads

- Python
Published by jon-xu over 7 years ago