From 5deb8dd8c39cb2917f29bea5829493f12f086e92 Mon Sep 17 00:00:00 2001 From: weiju Date: Wed, 13 Mar 2024 10:08:54 -0700 Subject: [PATCH] updated README.md --- README.md | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 0ad897a..1d8bb08 100644 --- a/README.md +++ b/README.md @@ -11,13 +11,13 @@ you can access a Docker image with a full MINER installation at Docker Hub with the name ```weiju/isb-miner3``` ``` -$ docker pull weiju/isb-miner3 +docker pull weiju/isb-miner3 ``` ### Through pip ``` -$ pip install isb-miner3 +pip install isb-miner3 ``` ## Command Line Tools documentation @@ -26,26 +26,26 @@ Please see command line documentation at https://baliga-lab.github.io/miner3/ ## Tutorial information -Find a walkthrough analysis in the form of a [Jupyter Notebook here](Example MINER Analysis.ipynb) +Find a walkthrough analysis in the form of a [Jupyter Notebook here](Example%20MINER%20Analysis.ipynb) ## What you need to get started Before the miner analysis can be performed, the gene expression data to be analyzed must be added to the miner/data directory. Ensure that your expression data is of the form log2(TPM+1) or log2(FPKM+1). - * If survival analysis is desired, a survival file must added to the miner/data directory - * If causal analysis is desired, a mutation file must added to the miner/data directory + * If survival analysis is desired, a survival file must added to the miner/data directory + * If causal analysis is desired, a mutation file must added to the miner/data directory ## Where to put your data miner will search for specific filenames in the miner/data folder. Be sure to update the lines that read your files with the appropriate paths and filenames. Consider using the following names for consistency: - 1. Name your expression data "expressionData.csv" - 2. Name your mutation data "mutations.csv" (only for causal analysis) - 3. Name your survival data "survival.csv" (only for survival analysis) + 1. Name your expression data "expressionData.csv" + 2. Name your mutation data "mutations.csv" (only for causal analysis) + 3. Name your survival data "survival.csv" (only for survival analysis) Note that the gene names will be converted to Ensembl Gene ID format ## Common mistakes to avoid - 1. miner does not yet support expression data in counts format. Ensure that data is in log2(TPM+1) or log2(FPKM+1) format. - 2. mechanistic inference includes a step that enforces a minimum correlation coefficient. If your results seem too sparse, try decreasing the minCorrelation parameter. + 1. miner does not yet support expression data in counts format. Ensure that data is in log2(TPM+1) or log2(FPKM+1) format. + 2. mechanistic inference includes a step that enforces a minimum correlation coefficient. If your results seem too sparse, try decreasing the minCorrelation parameter.