Rich Jones Miserlou
Miserlou
/ brain_fails.txt
Created
June 20, 2018 20:16
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| ~/Projects/gene-converter $ p build_and_convert.py | |
| docker build -t convert/elegene10st --build-arg package=pd.elegene.1.0.st_3.12.0.tar.gz --build-arg db=elegene10st -f Dockerfile.pd . | |
| Sending build context to Docker daemon 3.904GB | |
| Step 1/13 : FROM convert/base | |
| ---> d958adf36199 | |
| Step 2/13 : WORKDIR /home/user | |
| Removing intermediate container a0118890d985 | |
| ---> 47b27a4c2473 | |
| Step 3/13 : USER root | |
| ---> Running in 475050347cd0 |
Miserlou
/ organism_internal.tsv
Created
June 13, 2018 20:14
We can make this file beautiful and searchable if this error is corrected: No tabs found in this TSV file in line 0.
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| organism internal_accession | |
| Homo sapiens hgu133plus2 | |
| Mus musculus mouse4302 | |
| Homo sapiens hgu133a | |
| Homo sapiens hugene10st | |
| Mus musculus mogene10st | |
| Rattus norvegicus rat2302 | |
| Homo sapiens hgu133a2 | |
| Homo sapiens hgu219 | |
| Homo sapiens hthgu133pluspm |
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| ## | |
| # Hacked together, sorry.. | |
| # Required CSVs were tediously exported manually from GEO web interface. | |
| ## | |
| import csv | |
| import json | |
| import requests | |
| import pdb | |
| import pprint |
Miserlou
/ all_accessions.txt
Created
June 12, 2018 16:15
All the accessions we support as of June 12, 2018
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| SRP004164 | |
| SRP085379 | |
| GSE62322 | |
| SRP030508 | |
| SRP030509 | |
| SRP030506 | |
| SRP030507 | |
| SRP030504 | |
| SRP030505 | |
| SRP030502 |
Miserlou
/ Zebrafish Deduped.txt
Created
May 11, 2018 16:45
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| SRP068364 | |
| SRP041343 | |
| E-GEOD-24528 | |
| SRP020008 | |
| SRP084292 | |
| E-GEOD-39842 | |
| SRP111553 | |
| SRP069839 | |
| SRP058956 | |
| GSE94532 |
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| # GPL1319 | |
| GSE1894 | |
| GSE1995 | |
| GSE3303 | |
| GSE3667 | |
| GSE4201 | |
| GSE4585 | |
| GSE4859 | |
| GSE4989 | |
| GSE5048 |
Miserlou
/ geo_platforms_with_organism.json
Created
May 9, 2018 14:43
geo_platforms_with_organism.json
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| [ | |
| { | |
| "gpl": "GPL570", | |
| "num_samples": 137985, | |
| "organism": "Homo sapiens", | |
| "title": "[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array" | |
| }, | |
| { | |
| "gpl": "GPL13112", | |
| "num_samples": 99869, |
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| [ | |
| { | |
| "gpl": "GPL570", | |
| "num_samples": 137981, | |
| "title": "[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array" | |
| }, | |
| { | |
| "gpl": "GPL13112", | |
| "num_samples": 99869, | |
| "title": "Illumina HiSeq 2000 (Mus musculus)" |
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| GSE10080 | |
| GSE10241 | |
| GSE10842 | |
| GSE11567 | |
| GSE11913 | |
| GSE11915 | |
| GSE12215 | |
| GSE12243 | |
| GSE12771 | |
| GSE13201 |
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| GSE7701 | |
| GSE7702 | |
| GSE9067 | |
| GSE9187 | |
| GSE10057 | |
| GSE10107 | |
| GSE10864 | |
| GSE10956 | |
| GSE10959 | |
| GSE11132 |