From 4ee419c7cc9e0b6e968833e3ea30e8ce31bb927e Mon Sep 17 00:00:00 2001 From: Jared Andrews Date: Thu, 25 Mar 2021 17:57:34 -0500 Subject: [PATCH] Add ROSE links. --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 403096f..005beff 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # rosewater -**rosewater** assigns genes to (super-) enhancers output from ROSE in an expression-aware manner. It allows users to set a TPM threshold to filter genes that are not expressed on a sample-by-sample basis. +**rosewater** assigns genes to (super-) enhancers output from [ROSE](https://bitbucket.org/young_computation/rose/src/master/) in an expression-aware manner. It allows users to set a TPM threshold to filter genes that are not expressed on a sample-by-sample basis. ## Installation @@ -10,7 +10,7 @@ ## Usage -`rosewater` is fairly simple to use. It requires an annotation GTF file, a TSV file of TPMs with the gene name column named 'gene' (these should match the 'gene_name' attributes in the annotation GTF), the name of the sample column in the TPM file, and an output file from [ROSE](). Optionally, users can set a TPM threshold (set to 5 by default) for filtering out lowly/non-expressed genes prior to assignment. +`rosewater` is fairly simple to use. It requires an annotation GTF file, a TSV file of TPMs with the gene name column named 'gene' (these should match the 'gene_name' attributes in the annotation GTF), the name of the sample column in the TPM file, and an output file from [ROSE](https://bitbucket.org/young_computation/rose/src/master/). Optionally, users can set a TPM threshold (set to 5 by default) for filtering out lowly/non-expressed genes prior to assignment. ``` Usage: rosewater [OPTIONS]