Merge branch 'pub' of https://github.com/Zhiwen-Owen-Jiang/HEIG into pub

README.md

@@ -1,14 +1,16 @@
 # Highly Efficient Imaging Genetics (HEIG)
-HEIG is a statistical framework for efficiently conducting joint analysis for large-scale imaging and genetic data. Compared to traditional methods, HEIG reduces computational time and storage burden by over 100 times, significantly boosts statistical power in association analysis, and most importantly, defines the standard to share the voxel-level GWAS summary statistics to the community. 
+HEIG is a statistical framework for efficiently conducting joint analysis for large-scale imaging and genetic data. Compared to traditional methods, HEIG reduces computational time and storage burden by over 200 times, significantly boosts statistical power in association analysis, and most importantly, defines the standard to share the voxel-level GWAS summary statistics to the community. 
 
 The analysis can be performed by HEIG (will have more in the near future):
-- Voxelwise genome-wide association analysis (VGWAS)
+- Voxelwise genome-wide association analysis (VGWAS), including effcient GWAS for high-dimensional non-imaging phenotypes
 - Voxelwise heritability analysis
 - Genetic correlation analysis for pairs of voxels
 - Cross-trait genetic correlation between voxels and non-imaging phenotypes
 
 ## Version
-- [v1.1.0](https://github.com/Zhiwen-Owen-Jiang/heig/releases/tag/v1.1.0): Support multi-threading computation; many changes in data format; not compatible with v1.0.0.
+- [v1.0.0](https://github.com/Zhiwen-Owen-Jiang/heig/releases/tag/v1.0.0): initial version of HEIG.
+- [v1.1.0](https://github.com/Zhiwen-Owen-Jiang/heig/releases/tag/v1.1.0): support multi-threading computation; many changes in data format; not compatible with v1.0.0.
+- [v1.2.0](https://github.com/Zhiwen-Owen-Jiang/heig/releases/tag/v1.2.0): support LDR GWAS; provide more data mangement options; fix bugs in v1.1.0.
 
 ## System Requirements
 ### OS Requirements
@@ -20,21 +22,28 @@ HEIG is supported for macOS and Linux. It has been tested on the following syste
 HEIG is implemented in Python 3.11. Specific package dependencies are provided in [requirements](https://github.com/Zhiwen-Owen-Jiang/heig/blob/pub/requirements.txt).
 
 ## Getting Started
-First download the [released version](https://github.com/Zhiwen-Owen-Jiang/heig/releases/tag/v1.1.0), unzip it, and navigate to the extracted folder:
+First download the [released version](https://github.com/Zhiwen-Owen-Jiang/heig/releases/tag/v1.2.0), unzip it, and navigate to the extracted folder:
 ```
-wget -O heig-1.1.0.zip  https://github.com/Zhiwen-Owen-Jiang/heig/archive/refs/tags/v1.1.0.zip
-unzip heig-1.1.0.zip
-cd heig-1.1.0
+wget -O heig-1.2.0.zip  https://github.com/Zhiwen-Owen-Jiang/heig/archive/refs/tags/v1.2.0.zip
+unzip heig-1.2.0.zip
+cd heig-1.2.0
 ```
 Install [Miniconda](https://docs.anaconda.com/free/miniconda/miniconda-install/) based on your OS, and build the environment and install all dependencies for HEIG. This step may take ~5 minutes.
 ```
 conda env create --file environment.yml
 conda activate heig
 ```
-Or you can do it manually. 
+Or you can create a new environment and install dependencies through `pip`
+```
+conda create --name heig python=3.11
+conda activate myenv
+pip install -r requirements.txt
+```
+Since version v1.2.0, [hail](https://hail.is) has been a dependency for conducting GWAS analysis. If you fail to install hail, please contact the hail team.
+
 
 ## How to use HEIG
-We provided detailed [tutorial](https://github.com/Zhiwen-Owen-Jiang/heig/wiki) for using HEIG. The example data used in the tutorial for v1.1.0 can be downloaded [here](https://zenodo.org/records/13770930). Common issues are described in the [FAQ](https://github.com/Zhiwen-Owen-Jiang/heig/wiki/FAQ).
+We provided detailed [tutorial](https://github.com/Zhiwen-Owen-Jiang/heig/wiki) for using HEIG. The example data used in the tutorial for v1.2.0 can be downloaded [here](https://zenodo.org/records/14214075). Common issues are described in the [FAQ](https://github.com/Zhiwen-Owen-Jiang/heig/wiki/FAQ).
 
 If that does not work, email Owen Jiang <[email protected]> or <[email protected]>.