From b35e5df4dbb09776898c8a582e8e1dcca7d7158d Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 14 Apr 2025 20:57:51 -0700
Subject: [PATCH 1/2] README update

---
 README.md             | 28 ++++++++++++++------
 vignettes/Install.Rmd | 61 -------------------------------------------
 2 files changed, 20 insertions(+), 69 deletions(-)
 delete mode 100644 vignettes/Install.Rmd

diff --git a/README.md b/README.md
index 457f5c0..d965fcb 100644
--- a/README.md
+++ b/README.md
@@ -6,15 +6,8 @@ This R package implements ColocBoost --- motivated and designed for colocalizati
 
 ## Installation
 
-### Conda
-Install major releases from conda (recommended)
-
-```bash
-conda install -c dnachun r-colocboost
-```
-
 ### CRAN
-Install released versions from cran
+Install released versions from CRAN - precompiled packages are available on macOS and Windows
 
 ```r
 install.packages("colocboost")
@@ -27,6 +20,25 @@ Install the development version from GitHub
 devtools::install_github("StatFunGen/colocboost")
 ```
 
+### Conda
+Install major releases using a conda-compatible package manager (recommended)
+
+Global pixi installation is the easiest way to use the conda package
+```bash
+pixi global install r-base # Install r-base as a global package if not already installed
+pixi global install --environment r-base r-colocboost # Inject r-colocboost into r-base global environment
+```
+The package can also be added to a local pixi environment
+```bash
+pixi workspace channel add dnachun # Add the dnachun channel to the workspace
+pixi add r-colocboost # Add r-colocboost as a dependency to the environment
+```
+Micromamba is recommended instead of conda or mamba for traditional conda environments
+```bash
+micromamba install -c dnachun r-colocboost
+mamba install -c dnachun r-colocboost
+conda install -c dnachun r-colocboost
+```
 ## Usage
 
 ### Single-trait Fine-mapping (FineBoost)
diff --git a/vignettes/Install.Rmd b/vignettes/Install.Rmd
deleted file mode 100644
index 236ba9f..0000000
--- a/vignettes/Install.Rmd
+++ /dev/null
@@ -1,61 +0,0 @@
----
-title: "Installation Instructions for ColocBoost"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{Installation Instructions for ColocBoost}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-To install Seurat, [R](https://www.r-project.org/) version 4.0 or greater is required. We also recommend installing [R Studio](https://posit.co/).
-
-
-Seurat is available on [CRAN](https://cran.r-project.org/package=colocboost)??? for all platforms. To install, run: 
-
-```{r, eval = FALSE}
-# Enter commands in R (or R studio, if installed)
-install.packages('colocboost')
-library(colocboost)
-```
-
-The required dependences are
-
-```{r, eval = FALSE}
-if (!require("Rfast", quietly = TRUE))
-    install.packages("Rfast")
-if (!require("matrixStats", quietly = TRUE))
-    install.packages("matrixStats")
-if (!require("BiocManager", quietly = TRUE))
-    install.packages("BiocManager")
-BiocManager::install("qvalue")
-```
-
-
-# Install the development version of ColocBoost from GitHub
-
-Install the development version of ColocBoost - directly from [GitHub](https://github.com/StatFunGen/colocboost).
-
-```{r eval = FALSE}
-# Enter commands in R (or R studio, if installed)
-# Install the remotes package
-install.packages('remotes')
-remotes::install_github(repo = 'xueweic/colocboost')
-library(colocboost)
-```
-
-
-# Docker???
-
-We provide docker images for ColocBoost via [dockerhub](???).
-
-To pull the latest image from the command line:
-
-```sh
-docker pull xueweic/colocboost:latest
-```
-
-To use as a base image in a new Dockerfile:
-
-```sh
-FROM xueweic/colocboost:latest
-```

From 982bf04d1a362ec2ac9af0680fa89751b3286139 Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 14 Apr 2025 21:03:07 -0700
Subject: [PATCH 2/2] README update

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index d965fcb..01c3075 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@ This R package implements ColocBoost --- motivated and designed for colocalizati
 ## Installation
 
 ### CRAN
-Install released versions from CRAN - precompiled packages are available on macOS and Windows
+Install released versions from CRAN - pre-built packages are available on macOS and Windows
 
 ```r
 install.packages("colocboost")
@@ -21,7 +21,7 @@ devtools::install_github("StatFunGen/colocboost")
 ```
 
 ### Conda
-Install major releases using a conda-compatible package manager (recommended)
+Install major releases using pre-built conda package with a conda-compatible package manager (recommended)
 
 Global pixi installation is the easiest way to use the conda package
 ```bash