Vince Carey vjcitn
vjcitn
/ script.r
Last active
June 21, 2025 11:20
— forked from mvdbeek/script.r
sample for generating a simple csv
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| library(GBCC.mcm) | |
| library(SummarizedExperiment) | |
| library(SpatialFeatureExperiment) # includes localResults method | |
| x = GBCC.mcm::process_mcmicro("input.h5ad") | |
| expr_matrix <- assay(x, "X") | |
| expr_df <- as.data.frame(t(expr_matrix)) # Transpose so cells are rows | |
| # Get cell metadata | |
| metadata <- as.data.frame(colData(x)) | |
| # Get spatial coordinates | |
| coords <- as.data.frame(spatialCoords(x)) |
vjcitn
/ omicidx-beta-graphql-intro.ipynb
Created
March 21, 2019 11:00
— forked from seandavi/omicidx-beta-graphql-intro.ipynb
Quick introduction to the OmicIDX GraphQL API
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vjcitn
/ Dockerfile
Created
March 21, 2019 11:00
— forked from seandavi/Dockerfile
Dockerfile for blog post on using GCR. Builds SRA-toolkit with dbGaP access as an example
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| FROM ubuntu:18.04 | |
| RUN apt-get update | |
| RUN apt-get install -y wget | |
| # We do things this way to keep the docker image | |
| # size down. See https://nickjanetakis.com/blog/docker-tip-3-chain-your-docker-run-instructions-to-shrink-your-images | |
| RUN wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.2/sratoolkit.2.9.2-ubuntu64.tar.gz \ | |
| && tar -xvzf sratoolkit.2.9.2-ubuntu64.tar.gz \ | |
| && rm sratoolkit.2.9.2-ubuntu64.tar.gz |