NEWS.md

In shahcompbio/signals: Single Cell Genomes with Allele Specificity

signals 0.12.0

• option to input cells to use for phasing for each chromosome
• plotHeatmap with arbitrary annotation dataframe
• remove chrY

signals 0.11.4

• fix typo assigning A->B

signals 0.11.3

• catch negative state_AS issue for singleton bins

signals 0.11.2

• fix negative state_AS issue. This was caused during the fill missing step which assigns states with NA BAF values based on neighbouring bins. When there was a state transition between bins sometimes A+B>state.

signals 0.11.1

• for umap_clustering, default is now to not use PCA

signals 0.11.0

• updates to plotting
• male/female option
• filter some cell for second pass phasing but do not remove
• do not remove cells by default if they have low coverage
• keep cells with large hom-dels

signals 0.10.0

• add chr string check
• remove acrocentric chromosomes in arm consensus
• minor changes to heatmap and plotting

signals 0.9.1

• Update docker to install suggests packages

signals 0.9.0

• Fix phasing issue that happens when the cluster identified to phase relative to has a diploid region

signals 0.8.0

• Add option to mask bins during inference

signals 0.7.6

• Fix bug in plot_clusters_used_for_phasing

signals 0.7.5

• Fixed r cmd check

signals 0.7.4

signals 0.7.3

signals 0.7.2

• release for zenodo

signals 0.7.1

signals 0.7.0

• change name to signals
• multiple updates to plotting
• rewrite of scRNAseq

signals 0.6.2

• fix missing argument

signals 0.6.1

• changed colours
• fill in missing bins
• improved documentation about inputs

signals 0.6.0

• add option to remove noisy cells from phasing

signals 0.5.5

• update plotting and clustering

signals 0.5.4

• update docker

signals 0.5.3

• some small updates to plotting and default params

signals 0.5.2

• update to vignette and plotting

signals 0.5.1

• updated default parameters

signals 0.5.0

• update ascn inference

signals 0.4.3

• filtering utility function

signals 0.4.2

• fix bug with filtering

signals 0.4.1

• Fix bug in HMM when total copy number = 0
• Add function to filter hscn object

signals 0.4.0

• Add option to filter haplotypes
• Added Dockerfile and github actions to push to Dockerhub
• Added QC metadata table to output

signals 0.3.0

• Version associated with preprint
• some fixes to plotting

signals 0.2.1

• updates to heatmap plotting

signals 0.2.0

signals 0.1.0

• Added a NEWS.md file to track changes to the package.

shahcompbio/signals documentation built on Jan. 11, 2025, 2:20 a.m.