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@@ -37,7 +37,9 @@ _tools that you do not need to use directly as they have binding functions in ge | |
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`pip install broad-genepy` | ||
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and then use with `from genepy.utils/epigenetics/... import ...` | ||
and then use with `from genepy.utils/epigenetics/... import ...` | ||
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Please see the next step to get access to all bindings and tools. | ||
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### dev mode | ||
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@@ -56,30 +58,33 @@ from genepy.epigenetics import chipseq | |
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``` | ||
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## data: | ||
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hg38 genome sizes: from https://github.com/igvteam/igv/blob/master/genomes/sizes/hg38.chrom.sizes | ||
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## installation: to get access to all bindings | ||
## installation: to get access to all bindings and tools | ||
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Install the following tools: | ||
- [gcloud](https://cloud.google.com/sdk/docs/install-sdk) | ||
- [firecloud-dalmatian](https://github.com/getzlab/dalmatian) | ||
- [gsheets](https://github.com/xflr6/gsheets) | ||
- [htslib/samtools](http://www.htslib.org/) | ||
- [bwa](https://github.com/lh3/bwa) | ||
just used once: | ||
- [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) | ||
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Some of these packages like gsheets, gcloud, firecloud-dalmatian will require you to create google accounts, login on your machine or download oauth files. | ||
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Finaly you can install R packages (GSEABase, erccdashboard, GSVA, DESeq2): | ||
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```bash | ||
R -e 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")};BiocManager::install(c("GSEABase", "erccdashboard", "GSVA", "DESeq2"));' | ||
``` | ||
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## data: | ||
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hg38 genome sizes: from https://github.com/igvteam/igv/blob/master/genomes/sizes/hg38.chrom.sizes | ||
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## About | ||
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please do contribute, we do not have time to fix all issues or work on feature requests | ||
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Jeremie Kalfon [email protected] [email protected] https://jkobject.com | ||
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Javad Noorbakhsh [email protected] | ||
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Apache license 2.0. |