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@armish
armish / minibucket.ipynb
Created Jun 26, 2017
Experimenting with direct use of buckets for the cohorts-level analyses
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@armish
armish / gdc_download.ml
Last active Apr 4, 2017
Experiments with replacing gdc-client with a ketrew workflow
View gdc_download.ml
#use "topfind";;
#thread
#use "biokepi_machine.ml";;
open Biokepi
open KEDSL
open Cmdliner
(* simple aliases *)
View keybase.md

Keybase proof

I hereby claim:

  • I am armish on github.
  • I am armish (https://keybase.io/armish) on keybase.
  • I have a public key ASCZY1H-Zg-Yt8dFqLLOAdRtNJPEvhilMDnwYwWAfaZTpQo

To claim this, I am signing this object:

@armish
armish / Dockerfile.pyensembl
Created Jul 27, 2016
Docker image with all genomes cached via pyensembl in it
View Dockerfile.pyensembl
# This Docker image is meant to serve commonly used Ensembl Genomes
# already cached via PyEnsembl. Any application that depends on
# the pyensembl library can use this image to speed things up
# as caching these genomes is a huge bottleneck for most applications
FROM ubuntu:latest
MAINTAINER B. Arman Aksoy <arman@aksoy.org>
## We will be needing a few utilities to get this going
@armish
armish / fastqc_to_email.sh
Created Jul 15, 2016
A script to summarize FASTQC results to be included in an email.
View fastqc_to_email.sh
#!/bin/bash
# Usage:
# $ bash fastqc_to_email.sh REPORT_HEADER /path/to/file1.html /path/to/file2.html ...
#
# requires the unzipped folder containing the summaries to be present in the same folder
# with the HTML report!
JOB_NAME=$1
echo "# FASTQC ran for $JOB_NAME"
@armish
armish / dna_repair_molecules.tsv
Created Jun 17, 2016
Reactome - DNA Repair molecules (all)
View dna_repair_molecules.tsv
MoleculeType Identifier MoleculeName
Chemical Compounds 15414 S-adenosyl-L-methionine [ChEBI:15414]
Chemical Compounds 16680 S-adenosyl-L-homocysteine [ChEBI:16680]
Chemical Compounds 15351 acetyl-CoA [ChEBI:15351]
Chemical Compounds 17154 nicotinamide [ChEBI:17154]
Chemical Compounds 16960 ADP-D-ribose [ChEBI:16960]
Chemical Compounds 15377 water [ChEBI:15377]
Chemical Compounds 15422 ATP [ChEBI:15422]
Chemical Compounds 15846 NAD(+) [ChEBI:15846]
Chemical Compounds 15379 dioxygen [ChEBI:15379]
@armish
armish / tcga_purity_vaf.ipynb
Created May 24, 2016
TCGA - purity estimation from VAF
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@armish
armish / studies.ipynb
Created May 6, 2016
Getting a list of all TCGA studies and their abbreviations via pytcga
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@armish
armish / sampleData.R
Created Apr 27, 2016
Multi-level coffeewheel data
View sampleData.R
sampleWheelData <- list(
list(
name="R",
children=list(
list(
name="R_1",
children=list(
list(name="R_1_1", colour="#160000"),
list(name="R_1_2", colour="#220000"),
list(name="R_1_3", colour="#280000")
View Feather - Python.ipynb
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