Recent changes to README

README modified by Burton Chia

Burton Chia — Fri, 11 Dec 2015 03:24:28 -0000

--- v10
+++ v11
@@ -105,6 +105,13 @@

+-----------------
+Citing OncoIMPACT
+-----------------
+Bertrand _et. al._. __Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.__ [_Nucleic Acid Research_ 2015, 43 (7): e44](http://nar.oxfordjournals.org/content/43/7/e44.long)
+
+
+
 --------
 Contacts
 --------

README modified by Chayaporn Suphavilai

Chayaporn Suphavilai — Fri, 10 Jul 2015 02:46:53 -0000

--- v9
+++ v10
@@ -1,9 +1,9 @@
 -----------
 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 a first-in-class algorithmic framework that nominates patient-specific driver genes by integrative modeling of 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 parameter settings from the data sets provided and (2) a discovery mode where information in the provided database is used to predict driver genes for each sample in an additional data set (which can be the same as the one used to create the database).
+OncoIMPACT is configured to run in two modes: (1) a database mode that allows it to determine parameter settings from the data sets provided and (2) a discovery mode where information in the provided database is used to predict driver genes for samples in an additional data set from the same cancer type.

 ------------
 Installation
@@ -20,14 +20,14 @@

 __Input file format__

-- _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.
+- _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.
+- _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 specific project. The config file needs to contain the following parameters (you may refer to the sample config file provided with the scripts under <_Scripts Directory/sampleConfig.cfg_\>).
+You will need to create a configuration file for your specific project. The configuration file needs to contain the following parameters (you may refer to the sample configuration file provided with the scripts under <_Scripts Directory/sampleConfig.cfg_\>).

 - _outDir_: Full path to destination folder

@@ -35,13 +35,13 @@

 - _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

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

@@ -51,7 +51,7 @@

 When you are ready to run the OncoIMPACT pipeline, simply enter the following command
-   _oncoIMPACT.pl _
+   _oncoIMPACT.pl _

 -----------
 Sample data
@@ -62,7 +62,7 @@

 - _Glioblastoma_database.tgz_: pre-computed database of the TCGA GBM dataset

-- _single_patient.tgz_: data for a single single GBM patient (to test the discovery mode)
+- _single_patient.tgz_: data for a single GBM patient (to test the discovery mode)

 ----------
@@ -80,7 +80,7 @@

 __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_: An 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

README modified by Burton Chia

Burton Chia — Thu, 26 Mar 2015 02:43:59 -0000

--- v8
+++ v9
@@ -112,4 +112,4 @@

 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 Burton Chia (<chiakhb@gis.a-star.edu.sg>).
+If you have other questions or feedback, you may direct them to Denis Bertrand (<bertrandd@gis.a-star.edu.sg>) and Burton Chia (<chiakhb@gis.a-star.edu.sg>).

README modified by Burton Chia

Burton Chia — Thu, 05 Mar 2015 08:56:27 -0000

--- v7
+++ v8
@@ -2,6 +2,7 @@
 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 parameter settings from the data sets provided and (2) a discovery mode where information in the provided database is used to predict driver genes for each sample in an additional data set (which can be the same as the one used to create the database).

 ------------

README modified by Burton Chia

Burton Chia — Thu, 05 Mar 2015 08:56:02 -0000

--- v6
+++ v7
@@ -19,11 +19,11 @@

 __Input file format__

-- _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.
+- _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.
+- _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.
+- _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 specific project. The config file needs to contain the following parameters (you may refer to the sample config file provided with the scripts under <_Scripts Directory/sampleConfig.cfg_\>).

README modified by Denis Bertrand

Denis Bertrand — Thu, 05 Mar 2015 08:51:31 -0000

--- v5
+++ v6
@@ -1,15 +1,15 @@
 -----------
 What is it?
 -----------
-Cancer-omics Data Integration pipeline
-
+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 parameter settings from the data sets provided and (2) a discovery mode where information in the provided database is used to predict driver genes for each sample in an additional data set (which can be the same as the one used to create the database).

 ------------
 Installation
 ------------
 Download and uncompress the latest version
    _tar -zxvf oncoIMPACT.tgz_
-        _chmod +x oncoIMPACT_v0.9.2/*.pl_
+        _chmod +x oncoIMPACT_v0.9.3/*.pl_

 -----
 Usage
@@ -19,17 +19,16 @@

 __Input file format__

-- _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 CNV data is not available for that particular sample.
+- _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_: 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.
+- _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 log fold-change value.
-
+- _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 specific project. The config file needs to contain the following parameters (you may refer to the sample config file provided with the scripts under <_Scripts Directory/sampleConfig.cfg_\>).

-- _outDir_: Full path to destination folder. Two sub-folders will be created in this directory: INCOMPLETE_SAMPLES (for incomplete samples) and COMPLETE_SAMPLES (for complete samples)    
+- _outDir_: Full path to destination folder

 - _scriptDir_: Full path to folder where oncoIMPACT is installed

@@ -39,42 +38,54 @@

 - _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)

-
-When you are ready to run the oncoIMPACT pipeline, simply enter the following command
-   _oncoIMPACT.pl  <fraction of="" samples="" used="" during="" parameters="" estimation\="">_
-   
-
+When you are ready to run the OncoIMPACT pipeline, simply enter the following command
+   _oncoIMPACT.pl _

 -----------
 Sample data
 -----------
-We have provided two sample datasets for to test the oncoIMPACT pipeline which you may download from the website https://sourceforge.net/projects/oncoimpact/files;
+We have provided 1 sample datasets for to test the OncoIMPACT pipeline;

-- _Glioblastoma.tgz_: Glioblastoma TCGA dataset
+- _Glioblastoma.tgz_: Glioblastoma (GBM) TCGA dataset

-- _Ovarian.tgz_: Ovarian cancer TCGA dataset
+- _Glioblastoma_database.tgz_: pre-computed database of the TCGA GBM dataset

-- To run OncoIMPACT on those dataset: _oncoIMPACT.pl  0.2_
+- _single_patient.tgz_: data for a single single GBM patient (to test the discovery mode)

 ----------
 Change Log
 ----------
+
+__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_: 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__:

README modified by Burton Chia

Burton Chia — Thu, 26 Feb 2015 05:11:35 -0000

--- v4
+++ v5
@@ -9,6 +9,7 @@
 ------------
 Download and uncompress the latest version
    _tar -zxvf oncoIMPACT.tgz_
+        _chmod +x oncoIMPACT_v0.9.2/*.pl_

 -----
 Usage

README modified by Burton Chia

Burton Chia — Wed, 25 Feb 2015 08:33:25 -0000

--- v3
+++ v4
@@ -40,6 +40,8 @@

 - _snp_: Full path to snp data matrix

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

 When you are ready to run the oncoIMPACT pipeline, simply enter the following command
@@ -63,14 +65,21 @@
 Change Log
 ----------
 __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 will complete in less than 2 hours on 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.
+
+- _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

README modified by Burton Chia

Burton Chia — Wed, 25 Feb 2015 08:27:03 -0000

--- v2
+++ v3
@@ -58,9 +58,28 @@

 - To run OncoIMPACT on those dataset: _oncoIMPACT.pl  0.2_

+
+----------
+Change Log
+----------
+__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 will complete in less than 2 hours on 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

README modified by Denis Bertrand

Denis Bertrand — Tue, 17 Feb 2015 01:48:36 -0000

--- v1
+++ v2
@@ -17,32 +17,33 @@

 __Input file format__
--_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 CNV data is not available for that particular sample.

--_SNP data_: 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.
+- _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 CNV data is not available for that particular sample.

--_EXP data_: a tab-separated file with samples as columns and genes as rows. Each entry of this matrix would represent the log fold-change value.
+- _SNP data_: 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 log fold-change value.

 __Config file__
 You will need to create a config file for your specific project. The config file needs to contain the following parameters (you may refer to the sample config file provided with the scripts under <_Scripts Directory/sampleConfig.cfg_\>).

--_outDir_: Full path to destination folder. Two sub-folders will be created in this directory: INCOMPLETE_SAMPLES (for incomplete samples) and COMPLETE_SAMPLES (for complete samples) 
+- _outDir_: Full path to destination folder. Two sub-folders will be created in this directory: INCOMPLETE_SAMPLES (for incomplete samples) and COMPLETE_SAMPLES (for complete samples)    

--_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

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

 When you are ready to run the oncoIMPACT pipeline, simply enter the following command
-   _oncoIMPACT.pl _
+   _oncoIMPACT.pl  <fraction of="" samples="" used="" during="" parameters="" estimation\="">_

@@ -50,11 +51,12 @@
 Sample data
 -----------
 We have provided two sample datasets for to test the oncoIMPACT pipeline which you may download from the website https://sourceforge.net/projects/oncoimpact/files;
--_Glioblastoma.tgz_: Glioblastoma TCGA dataset

--_Ovarian.tgz_: Ovarian cancer TCGA dataset
+- _Glioblastoma.tgz_: Glioblastoma TCGA dataset

+- _Ovarian.tgz_: Ovarian cancer TCGA dataset

+- To run OncoIMPACT on those dataset: _oncoIMPACT.pl  0.2_

 ---------
 Licensing