Kevin Stachelek whtns

## ensembl_vep_102_with_offline_cache.md

      
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                ckandoth
                / ensembl_vep_102_with_offline_cache.md
            
            
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              November 7, 2023 14:32
            
              
                Install Ensembl's VEP v102 with local cache for running offline
              
          
    Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.
Instead of the official instructions, we will use conda to install VEP and its dependencies. If you don't already have conda, install it into $HOME/miniconda3 as follows:
curl -sL https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh -o /tmp/miniconda.sh
sh /tmp/miniconda.sh -bfp $HOME/miniconda3
Add the conda bin folder into your $PATH so that all installed tools are accessible via command-line. You can also add this to your ~/.bashrc

  
## Seurat_to_velocyto.R
library(velocyto.R)
library(pagoda2)
library(Seurat)

### ASSUMES Seurat object has already been computed -- in this case the object cells.combined is the result of seurat

# IMPORTANT!!! create a loom file using the velocyto command line tools first
ldat <- read.loom.matrices("filtered.loom")

# get the spliced and unspliced ratios from the loom file

## ensembl_vep_95_with_offline_cache.md

      
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                ckandoth
                / ensembl_vep_95_with_offline_cache.md
            
            
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              October 4, 2022 21:49
            
              
                Install Ensembl's VEP v95 with various caches for running offline
              
          
    Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.
To follow these instructions, we'll assume you have these packaged essentials installed:
## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

  
## ensembl_vep_86_with_offline_cache.md

      
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                ckandoth
                / ensembl_vep_86_with_offline_cache.md
            
            
              Last active
              July 15, 2021 16:26
            
              
                Install Ensembl's VEP v86 with various caches for running offline
              
          
    Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.
To follow these instructions, we'll assume you have these packaged essentials installed:
## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel
	library(velocyto.R)
	library(pagoda2)
	library(Seurat)

	### ASSUMES Seurat object has already been computed -- in this case the object cells.combined is the result of seurat

	# IMPORTANT!!! create a loom file using the velocyto command line tools first
	ldat <- read.loom.matrices("filtered.loom")

	# get the spliced and unspliced ratios from the loom file