Recent changes to Home

Home modified by Koh Jia Yu

Koh Jia Yu — Fri, 09 Dec 2016 08:15:57 -0000

--- v11
+++ v12
@@ -59,16 +59,15 @@

 # Test datasets

-We have provided test datasets for the OncoIMPACT pipeline in 2 different ways.
+We have provided test datasets to try OncoIMPACT on its 2 different modes.

-**Database and discovery mode: sampleConfig_db_disc.cfg (config file)**
-
+**Database and discovery mode**: 
+sampleConfig_db_disc.cfg: config file
 Glioblastoma.tgz: Glioblastoma (GBM) TCGA dataset (this dataset should be uncompressed)

-**Discovery mode: sampleConfig_disc.cfg (config file)**
-
-single_patient.tgz: data for a single GBM patient (this dataset should be uncompressed)
-
+**Discovery mode**: 
+sampleConfig_disc.cfg:  config file
+single_patient.tgz: data of a single GBM patient (this dataset should be uncompressed)
 Glioblastoma_database.tgz: pre-computed database of the TCGA GBM dataset

Home modified by Koh Jia Yu

Koh Jia Yu — Fri, 09 Dec 2016 08:02:03 -0000

--- v10
+++ v11
@@ -31,25 +31,25 @@
 **Config file** 
 You will need to create a config file for your project. The config file needs to contain the following parameters (you may refer to the sample config file provided with the test datasets under TEST_DATASET/sampleConfig.cfg).

-outDir: Full path to destination folder
+**outDir:** Full path to destination folder

-scriptDir: Full path to folder where oncoIMPACT is installed
+**scriptDir:** Full path to folder where oncoIMPACT is installed

-numThreads: Number of threads to use
+**numThreads:** Number of threads to use

-cnv: Full path to cnv data matrix
+**cnv:** Full path to cnv data matrix

-exp: Full path to expression data matrix
+**exp:** Full path to expression data matrix

-dataType: Flag for expression data type. Vvalid options: ARRAY (default), RNA_SEQ
+**dataType:** Flag for expression data type. Vvalid options: ARRAY (default), RNA_SEQ

-snp: Full path to snp data matrix
+**snp:** Full path to snp data matrix

-dataBase: Full path to the pre-computed database **(implies discovery mode only)**
+**dataBase:** Full path to the pre-computed database **(implies discovery mode only)**

-databaseExport: Full path where the database will be exported **(implies database + discovery mode)**
+**databaseExport:** Full path where the database will be exported **(implies database + discovery mode)**

-testMode: Boolean flag to toggle test mode (valid options: 0 / 1)
+**testMode:** Boolean flag to toggle test mode (valid options: 0 / 1)

 ***at any one time, only one of either the options, <dataBase> or <databaseExport>, may be chosen to run oncoIMPACT.**

@@ -61,22 +61,15 @@

 We have provided test datasets for the OncoIMPACT pipeline in 2 different ways.

-**Database and discovery mode**
+**Database and discovery mode: sampleConfig_db_disc.cfg (config file)**

-sampleConfig_db_disc.cfg
+Glioblastoma.tgz: Glioblastoma (GBM) TCGA dataset (this dataset should be uncompressed)

--Glioblastoma.tgz: 
-Glioblastoma (GBM) TCGA dataset (the full cnv/exp/snp data is needed when running in database + discovery mode)
+**Discovery mode: sampleConfig_disc.cfg (config file)**

-**Discovery mode**
+single_patient.tgz: data for a single GBM patient (this dataset should be uncompressed)

-sampleConfig_disc.cfg
-
--single_patient.tgz: 
-data for a single GBM patient (this single patient cnv/exp/snp data can only be used when running in discovery mode)
-
--Glioblastoma_database.tgz: 
-pre-computed database of the TCGA GBM dataset
+Glioblastoma_database.tgz: pre-computed database of the TCGA GBM dataset

 # Change Log

Home modified by Koh Jia Yu

Koh Jia Yu — Fri, 09 Dec 2016 06:40:27 -0000

--- v9
+++ v10
@@ -2,7 +2,7 @@

 [[download_button]]

-
+***
 # What is it?

 OncoIMPACT is a first-in-class algorithmic framework that nominates patient-specific driver genes by integratively modeling genomic mutations (point, structural and copy-number) and the resulting perturbations in transcriptional programs via defined molecular networks.

Home modified by Koh Jia Yu

Koh Jia Yu — Fri, 09 Dec 2016 06:40:01 -0000

--- v8
+++ v9
@@ -1,7 +1,7 @@
 Welcome to oncoIMPACT. Thank you for taking some time to read through this wiki entry to know more about running oncoIMPACT.

 [[download_button]]
-***
+

 # What is it?

Home modified by Koh Jia Yu

Koh Jia Yu — Fri, 09 Dec 2016 06:36:40 -0000

--- v7
+++ v8
@@ -1,6 +1,7 @@
 Welcome to oncoIMPACT. Thank you for taking some time to read through this wiki entry to know more about running oncoIMPACT.

 [[download_button]]
+***

 # What is it?

Home modified by Koh Jia Yu

Koh Jia Yu — Fri, 09 Dec 2016 06:36:11 -0000

--- v6
+++ v7
@@ -1,4 +1,6 @@
 Welcome to oncoIMPACT. Thank you for taking some time to read through this wiki entry to know more about running oncoIMPACT.
+
+[[download_button]]

 # What is it?

@@ -56,20 +58,25 @@

 # Test datasets

-We have provided test datasets for the OncoIMPACT pipeline;
+We have provided test datasets for the OncoIMPACT pipeline in 2 different ways.

-**sampleConfig_disc.cfg:** sample config for discovery mode
+**Database and discovery mode**

-. single_patient.tgz: 
+sampleConfig_db_disc.cfg
+
+-Glioblastoma.tgz: 
+Glioblastoma (GBM) TCGA dataset (the full cnv/exp/snp data is needed when running in database + discovery mode)
+
+**Discovery mode**
+
+sampleConfig_disc.cfg
+
+-single_patient.tgz: 
 data for a single GBM patient (this single patient cnv/exp/snp data can only be used when running in discovery mode)

-. Glioblastoma_database.tgz: 
+-Glioblastoma_database.tgz: 
 pre-computed database of the TCGA GBM dataset

-**sampleConfig_db_disc.cfg:** sample config for database and discovery mode
-
-. Glioblastoma.tgz: 
-Glioblastoma (GBM) TCGA dataset (the full cnv/exp/snp data is needed when running in database + discovery mode)

 # Change Log

@@ -115,4 +122,3 @@

 [[members limit=20]]
-[[download_button]]

Home modified by Koh Jia Yu

Koh Jia Yu — Fri, 09 Dec 2016 06:13:34 -0000

--- v5
+++ v6
@@ -50,7 +50,8 @@

 ***at any one time, only one of either the options, <dataBase> or <databaseExport>, may be chosen to run oncoIMPACT.**

-When you are ready to run the OncoIMPACT pipeline, simply enter the following command oncoIMPACT.pl 
+When you are ready to run the OncoIMPACT pipeline, simply enter the following command 
+*oncoIMPACT.pl path_to_config_file*
 ***

 # Test datasets

Home modified by Koh Jia Yu

Koh Jia Yu — Fri, 09 Dec 2016 06:10:33 -0000

--- v4
+++ v5
@@ -1,6 +1,116 @@
 Welcome to oncoIMPACT. Thank you for taking some time to read through this wiki entry to know more about running oncoIMPACT.

-[[include ref=README]]
+# What is it?
+
+OncoIMPACT is a first-in-class algorithmic framework that nominates patient-specific driver genes by integratively modeling genomic mutations (point, structural and copy-number) and the resulting perturbations in transcriptional programs via defined molecular networks.
+
+OncoIMPACT is configured to run in two modes: (1) a database mode that allows it to determine the parameter settings from the datasets provided (2) a discovery mode where information in the provided database is used to predict driver genes for each sample, in an additional data set.
+
+# Installation
+
+Download and uncompress the latest version 
+tar -zxvf oncoIMPACT.tgz 
+chmod +x oncoIMPACT_v0.9.4/*.pl
+
+# Usage
+
+Before running the pipeline, please have the following files ready.
+
+# Input files and formats
+
+CNV_data: a tab-separated file with samples as columns and genes as rows. Each entry of this matrix must hold either a value of -1/0/1. A value of -1 would indicate a DELETION event while a value of 1 will indicate an AMPLIFICATION event, and a value of 0 if the is not affected by copy number gene.
+
+SNP_data (point mutations and short indels): a tab-separated file with samples as columns and genes as rows. Each entry of this matrix must hold either the binary values of 0/1. A value of 1 would indicate the presence of a snp in the gene of that particular sample while a value of 0 would indicate otherwise.
+
+EXP_data: a tab-separated file with samples as columns and genes as rows. Each entry of this matrix would represent the log2 fold-change of the gene expression of the tumor compared to a normal control.
+***
+
+**Config file** 
+You will need to create a config file for your project. The config file needs to contain the following parameters (you may refer to the sample config file provided with the test datasets under TEST_DATASET/sampleConfig.cfg).
+
+outDir: Full path to destination folder
+
+scriptDir: Full path to folder where oncoIMPACT is installed
+
+numThreads: Number of threads to use
+
+cnv: Full path to cnv data matrix
+
+exp: Full path to expression data matrix
+
+dataType: Flag for expression data type. Vvalid options: ARRAY (default), RNA_SEQ
+
+snp: Full path to snp data matrix
+
+dataBase: Full path to the pre-computed database **(implies discovery mode only)**
+
+databaseExport: Full path where the database will be exported **(implies database + discovery mode)**
+
+testMode: Boolean flag to toggle test mode (valid options: 0 / 1)
+
+***at any one time, only one of either the options, <dataBase> or <databaseExport>, may be chosen to run oncoIMPACT.**
+
+When you are ready to run the OncoIMPACT pipeline, simply enter the following command oncoIMPACT.pl 
+***
+
+# Test datasets
+
+We have provided test datasets for the OncoIMPACT pipeline;
+
+**sampleConfig_disc.cfg:** sample config for discovery mode
+
+. single_patient.tgz: 
+data for a single GBM patient (this single patient cnv/exp/snp data can only be used when running in discovery mode)
+
+. Glioblastoma_database.tgz: 
+pre-computed database of the TCGA GBM dataset
+
+**sampleConfig_db_disc.cfg:** sample config for database and discovery mode
+
+. Glioblastoma.tgz: 
+Glioblastoma (GBM) TCGA dataset (the full cnv/exp/snp data is needed when running in database + discovery mode)
+
+# Change Log
+
+**v0.9.4:**
+
+NEW: Enable error checks
+
+**v0.9.3:**
+
+NEW: Enable the processing of RNA-seq data
+
+NEW: Enable the construction of databases
+
+NEW: Enable the discovery mode using a pre-computed database
+**
+v0.9.2:**
+
+NEW: Option in configuration file to run OncoIMPACT in test mode which performs the simulation with fewer iterations and fixed seed. In this mode, OncoIMPACT should complete in less than 2 hours using a single thread.
+
+NEW: Sanity checks to ensure validity of parameters provided by user
+
+FIX: Improved disk space utilization
+
+FIX: Improved compatibility with Mac OS.
+
+**v0.9.1:**
+
+oncoIMPACT will now avoid reproducing the input files if COMPLETE_SAMPLES folder exists
+
+fix for bugs introduced in last version
+
+# Licensing
+
+The MIT License (MIT) Copyright (c) 2014 Genome Institute of Singapore
+
+# Contacts
+
+If you want community-driven support, please visit the forum at https://sourceforge.net/p/oncoimpact/discussion/.
+
+If you have a bug to report, you may raise a ticket at https://sourceforge.net/p/oncoimpact/tickets/.
+
+If you have other questions or feedback, you may direct them to Jayce (kohjy@gis.a-star.edu.sg) and Denis (bertrandd@gis.a-star.edu.sg).

 [[members limit=20]]

Home modified by Burton Chia

Burton Chia — Tue, 23 Sep 2014 04:51:50 -0000

--- v3
+++ v4
@@ -1,4 +1,4 @@
-Welcome to oncoIMPACT. Do take some time to read through this wiki entry to know more about running oncoIMPACT.
+Welcome to oncoIMPACT. Thank you for taking some time to read through this wiki entry to know more about running oncoIMPACT.

 [[include ref=README]]

Home modified by Burton Chia

Burton Chia — Tue, 23 Sep 2014 04:51:10 -0000

--- v2
+++ v3
@@ -1,6 +1,6 @@
 Welcome to oncoIMPACT. Do take some time to read through this wiki entry to know more about running oncoIMPACT.

-
+[[include ref=README]]

 [[members limit=20]]