NEWS.md

In SingerLab/gac: Genetic Analysis of Cells

gac 0.0.9037

• improved functions to call copy number states from bulk DNA or Integer Copy Number

• calls can be exported as text (deletion, loss, gain, amplification) or with cbioportal notation, -2, -1, 0, +1, +2

• calls include an additional category representing > 20 copies of a gene. Term is high_amplification, and in cbioportal is labeled as +4

• added functions to estimate alteration frequencies in bulk DNA or Integer Copy Number

• added option to plot bins or gene alteration frequences

• minor changes for compatibility

gac 0.0.9036

• allow arguments to be passed down tho HeatmapAnnotation when implementing create_chromosome_annotation

• simplified create_chromosome_annotation base functions

• add_in_silico_root now exits if "X" contains cell.name e.g. 'diploid'

• adds plot_sK to inspect kParameter and kStable

• new method for assigning clusters in Bray Curtis Dissimilarity

gac 0.0.9035

• added function to add an in-silico root cell and clone

• bin.id checks between chrmoInfo and gene.index

• standardizing function names, renamed as export_cnr and summary_cnr

• pull_gene_details now pulls information from a gene list, rather than regions

gac 0.0.9034

• added functions to order bins and genes, and are implemented by default in sync_cnr

• added default colors to vdjHeatmap

• modified names of functions related to gene and region information lookup

• getting_started vignette cleanup

• copynumbers example data now matches that of the example cnr

gac 0.0.9033

• added features to allow FastME alogrithms for phylogenetic cell and clone pseudobulk reconstruction. Implemented via R/ape

gac 0.0.9032

• new sync_cnr function to resyncronize cnr tables after merge, etc This is now applied by default after running addCells, addPheno, and buildCNR

• adding default colors to heatmap plots

• debuged DDRC.g creation as there was a bug introduced and went missing

• added function to append information to the gene.index

• removing color map objects

gac 0.0.9031

• debug pull_gene_details and get_gene_details

gac 0.0.9030

• new split_cnr function to convert a cnr object into a list of cnr split by a categorical variable e.g. sample ID, treated vs control, etc.

gac 0.0.9029

• added option to change gene.type column in genotype_vdj

• changed seqnames column to chrom in gene index and matches chromInfo

• debugged other functions after setting gene.type.column

• cnr now uses default bioMart gene_biotype column name

gac 0.0.9028

• added code to estimate q-values in histology comparisons

gac 0.0.9027

• introduction of gene lookup functions based on coordinates

• further debugging to pass CRAN

gac 0.0.9026

• added functions to associate copy number to categorical phenotypes

• added functions to pull copy number froms specific genes

• added functions to visualize association resutls, e.g. manhattan plots, and effect plots

• added functions to convert from .seg Run Length Encoding (RLE) data to bin coordinates

• added functions to facilitate creating chromsome annotations for custom plots

• other helper functions

• removed @export tag in DepMap, OncoKB, and GISTIC2 specific functions

• tagged internal functions

• use of vegan::diversity rather than entropy::entropy

gac 0.0.9025

gac 0.0.9024

• added phyloDDRC among other functions

gac 0.0.9023

• minor fix to pass roundCNR arguments from buildCNR

gac 0.0.9022

• added clone assignment ranked by FGA and/or frequency

• added ability to root the cell phylogenetic tree

• added function to run clone phylogenetic analysis

gac 0.0.9021

• added VDJ clustering with Bray-Curtis Dissimilarity

• fixed vdj cell type in keepCells and excludeCells

gac 0.0.9020

• added support for subbsetting based on bins, genes, full chromosomes and genomic coordinates

• debugged build notes 0 errors ✔ | 0 warnings ✔ | 0 notes ✔

gac 0.0.9019

• added plot_frequencies to plot amplification and deletion frequencies

• in setBrayClusters, if tree.height is NULL, the minimum intersect between one-cell and multi-cell clusters is used by default as the tree.height

gac 0.0.9018

• section on preparing your data added to getting_started.Rmd

• minor debugging on warnings, and unit tests

• moved badge to maturing

gac 0.0.9017

• Added summaryCNR function

• debugged warnings and notes

gac 0.0.9016

• Added VDJ genotyping and visualization

• Progress status in consensusClusterCNR

gac 0.0.9013

• Added f(x) to pull information from the gene.index

gac 0.0.9013

• Added estimation of alteration frequencies at gene and bin level

• Deduplicated example bin to gene tracks

• Added DATASET.R to show how example data is generated

gac 0.0.9012

• Added chromosome tickmarks in HeatmapCNR

• Added support for consensus clustering

• Added support for K Spectral to select max number of stable clusters from consensus clustering

gac 0.0.9000

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

SingerLab/gac documentation built on March 23, 2024, 5:15 a.m.