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switched to GRanges update

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gavinha committed May 30, 2019
1 parent d8736da commit 9c45b4eb9e2e3a5cfd1e1be245b767186d6972d3
Showing with 8 additions and 4 deletions.
  1. +8 −4 README.md
@@ -10,7 +10,7 @@ Ha, G., et al. (2014). [TITAN: Inference of copy number architectures in clonal
Gavin Ha
Fred Hutchinson Cancer Research Center
contact: <gavinha@gmail.com> or <gha@fredhutch.org>
Date: January 2, 2019
Date: May 30, 2019
Website: [GavinHaLab.org](https://gavinhalab.org/)

## Table of Contents
@@ -23,16 +23,20 @@ Website: [GavinHaLab.org](https://gavinhalab.org/)
* [License](#software-license)

## Links
Snakemake Workflow: https://github.com/gavinha/TitanCNA/tree/master/scripts/snakemake
**Snakemake Workflow:** https://github.com/gavinha/TitanCNA/tree/master/scripts/snakemake
**10X Snakemake Workflow:** https://github.com/gavinha/TitanCNA_10X_snakemake
Google Groups: https://groups.google.com/forum/#!forum/titancna
TitanCNA website: http://compbio.bccrc.ca/software/titan/
KRONOS TITAN Workflow: https://github.com/MO-BCCRC/titan_workflow
Publication in Genome Research: http://genome.cshlp.org/content/24/11/1881

## News
(See [NEWS](NEWS) for previous version notes)

### May 30, 2019 - TitanCNA version 1.23.1
Addressed the issue of `RangedData` being deprecated by converting code to use `GRanges` from the `GenomicRanges` package.
New or modified functions:
- `wigToGRanges`: to load WIG files and store in `GRanges` object.
- `correctIntegerCN()`: performs allelic copy number (major/minor CN) adjustment.

### August 9, 2018
Improved parameter inference by handling errors and allowing EM to continue until convergence. This fixes runs that previously would fail because samples had very low tumor content.

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