From 3f239dc1f88a5a59644e79c44297ae5b2c293b0f Mon Sep 17 00:00:00 2001 From: sshuai Date: Wed, 12 Sep 2018 13:55:31 -0400 Subject: [PATCH] Update README and remove old quick start. --- README.md | 28 +++++++++++++++------------- docs/source/index.rst | 1 - docs/source/tutorial.rst | 2 +- 3 files changed, 16 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 11502e99..37ab65a1 100644 --- a/README.md +++ b/README.md @@ -7,29 +7,31 @@ [![Documentation Status](https://readthedocs.org/projects/driverpower/badge/?version=latest)](http://driverpower.readthedocs.io/en/latest/?badge=latest) [Installation](https://driverpower.readthedocs.org/en/latest/install.html) | -[Quick start](https://driverpower.readthedocs.org/en/latest/quick_start.html) | +[Tutorial](https://driverpower.readthedocs.org/en/latest/tutorial.html) | [Documentation](https://driverpower.readthedocs.org) DriverPower is a tool used to discover potential coding and non-coding cancer driver elements from tumour whole-genome or whole-exome somatic mutations. -## Installation -DriverPower requires Python >= 3.5 and some other packages. If you don't have Python 3.5 or higher, we recommend to install Python with [Anaconda](https://www.continuum.io/downloads). +## How to use DriverPower +If you only have somatic mutations (in hg19) at hand and +would like to find drivers in well-annotated regions. Please use our [example data](https://figshare.com/projects/DriverPower_Dataset/36065) +and follow the [tutorial](https://driverpower.readthedocs.org/en/latest/tutorial.html). -To install DriverPower, you can either download and install it from [Python Package Index (PyPI)](https://pypi.python.org/pypi/DriverPower/) by typing the following command in your terminal -```bash -$ pip install driverpower -``` -or download the [latest source](https://github.com/smshuai/DriverPower/releases/latest/) to install. For example, to install version 1.0.0: -```console -$ tar -xzf DriverPower-1.0.1.tar.gz -$ cd DriverPower-1.0.1/ && pip install . -``` -See more details at [installation](https://driverpower.readthedocs.org/en/latest/install.html). +## Citation +Please cite our paper when you use DriverPower in your study: + +- Shuai, S., Gallinger, S., Stein, L. D., PCAWG Drivers and Functional Interpretation Group & ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net. **DriverPower: Combined burden and functional impact tests for cancer driver discovery**. bioRxiv 215244 (2017). +[doi:10.1101/215244](https://doi.org/10.1101/215244]) + +Please cite the PCAWG driver paper as well when you use our example data in your study: + +- Rheinbay, E. et al. **Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes**. bioRxiv 237313 (2017). [doi:10.1101/237313](https://doi.org/10.1101/237313) ## License DriverPower is distributed under the terms of the [GNU General Public License 3.0](https://www.gnu.org/licenses/gpl-3.0.txt). ## Change log +- 2018/09/12: Release version 1.0.2, which has minor modification. - 2017/11/22: Release version 1.0.1, which has bugs fixes and improved performance. - 2017/08/03: Release version 1.0.0, which is used in our manuscript. - 2017/03/02: Release version 0.4.0, which is used in the PCAWG driver analysis. diff --git a/docs/source/index.rst b/docs/source/index.rst index 50e10638..150c91d6 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -7,7 +7,6 @@ DriverPower: a tool for computational cancer driver discovery tutorial install - quick_start command_line data_format diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst index be434c92..d01617cb 100644 --- a/docs/source/tutorial.rst +++ b/docs/source/tutorial.rst @@ -165,7 +165,7 @@ Here we show how to score 1,000 mutations and calculate per-element score: # We omit INDELs here; but CADD can score INDELs in VCF format zcat ./random_mutations.tsv.gz | \ awk 'BEGIN{OFS="\t"} $4 != "-" && $5 != "-" {print $1,$3,".",$4,$5}' | \ - head -100000 | gzip > random_mutations.1K.vcf.gz + head -1000 | gzip > random_mutations.1K.vcf.gz # Upload formatted variants (random_mutations.1K.vcf.gz) to CADD's web interface # and download the result file (something like GRCh37-v1.4_f8600bd0c0aa23d4f6abc99eb8201222.tsv.gz). #####