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Christina Chatzipantsiou cgpu

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@cgpu
cgpu / metadata.csv
Created April 24, 2020 08:26
sample_id status
SRR10503928 control
SRR10503929 control
SRR10503936 case
SRR10503937 case
@cgpu
cgpu / metadata_real_accession.list
Last active April 30, 2020 01:00
SRR10503928
SRR10503929
SRR10503936
SRR10503937
SRR3623945
SRR3623944
SRR3623940
SRR3623941
@cgpu
cgpu / jupyter-example-repos.ipynb
Created April 21, 2020 21:01
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@cgpu
cgpu / metadata_masterfile.csv
Last active April 30, 2020 02:26
contrast metadata_file
few_real_samples https://gist.githubusercontent.com/cgpu/019614494177b84f9d64ec8552f66a15/raw/8ed0e0b344f513a796c19919824e15b7d45a2e2e/metadata.csv
cohort_18 https://gist.githubusercontent.com/cgpu/77d125fbab5022b84f5d39fe44368f01/raw/3f7c2ed65f1ca6ffb07b0cc68695cd64775fe2cb/cohort_18.csv
@cgpu
cgpu / metadata.csv
Last active April 23, 2020 17:02
sample_id status
SRR4238351 control
SRR4238355 control
SRR4238359 case
SRR4238379 case
@cgpu
cgpu / get_content.groovy
Created April 19, 2020 14:36 — forked from kdabir/get_content.groovy
get content from url and write to a file in groovy
// saving from url to a file (append)
new File("output.xml") << new URL ("http://some.url/some/path.xml").getText()
@cgpu
cgpu / sendmail_template.txt
Created April 19, 2020 02:26
To: $email
Subject: $subject
Mime-Version: 1.0
Content-Type: multipart/related;boundary="nfcoremimeboundary"
--nfcoremimeboundary
Content-Type: text/html; charset=utf-8
$email_html
@cgpu
cgpu / get_dupes_GTEX_ids.R
Last active April 9, 2020 18:00
Inspect duplicate ids in SAMPID column
# From yarn::downloadGtexV8
pData <- read.csv("pData_yarn_downloadGTExV8.csv")
# rMATS analysed
samples_sra <- as.vector(t(read.csv("samples.csv", header = FALSE)))
# From SraRunTable
meta.data <- read.csv("SraRunTable.noCram.noExome.noWGS.totalRNA.txt", header = T)
meta.data <- meta.data[meta.data$Run %in% samples_sra, ]
dim(meta.data)
@cgpu
cgpu / 2_RMATS_merging_masterfile.csv
Last active March 31, 2020 20:41
rmats-nf-5e8191d89dfe0b1bf3b148b0 gs://cloudosinputdata/team/5e601f9f786cca0107921955/user/5e601f9f786cca0107921954/projects/5e7900c786fdca01036e78a9/jobs/5e8191d89dfe0b1bf3b148b0/results/split_matrices.tar.gz
rmats-nf-5e7cd41bacc18a010409f1a6 gs://cloudosinputdata/team/5e601f9f786cca0107921955/user/5e601f9f786cca0107921954/projects/5e7900c786fdca01036e78a9/jobs/5e7cd41bacc18a010409f1a6/results/split_matrices.tar.gz
@cgpu
cgpu / 2_gs_files.csv
Created March 31, 2020 16:25
5e8191caef806a1bef41c706 gs://cloudosinputdata/team/5e601f9f786cca0107921955/user/5e601f9f786cca0107921954/projects/5e7900c786fdca01036e78a9/jobs/5e8191caef806a1bef41c706/results/split_matrices.tar.gz
5e8191e7c1a31e1bf69b03dc gs://cloudosinputdata/team/5e601f9f786cca0107921955/user/5e601f9f786cca0107921954/projects/5e7900c786fdca01036e78a9/jobs/5e8191e7c1a31e1bf69b03dc/results/split_matrices.tar.gz