Pierre Lindenbaum lindenb

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I hate people.

Institut-du-Thorax, Nantes, France.

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lindenb / Usage.md

Created September 10, 2020 12:23

Question: is there any way to filter NCBI datasets by sample type?

$ wget -q -O - "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19826&targ=self&form=xml&view=quick" |\
  xsltproc biostar460606.xsl - | bash
 
GSM495051 !Sample_source_name_ch1 = noncancer tissue
GSM495052 !Sample_source_name_ch1 = gastric cancer tissue
GSM495053 !Sample_source_name_ch1 = noncancer tissue
GSM495054 !Sample_source_name_ch1 = gastric cancer tissue
GSM495055 !Sample_source_name_ch1 = noncancer tissue
GSM495056 !Sample_source_name_ch1 = gastric cancer tissue

lindenb / biostar441624.txt

Created June 3, 2020 16:50

https://www.biostars.org/p/441624/ owl gwas

	http://www.ebi.ac.uk/efo/EFO_0003898 ankylosing spondylitis
	http://www.ebi.ac.uk/efo/EFO_0000783 myositis
	http://www.ebi.ac.uk/efo/EFO_1001806 macrophage activation syndrome
	http://www.ebi.ac.uk/efo/EFO_1001807 malacoplakia
	http://www.ebi.ac.uk/efo/EFO_1000719 juvenile dermatitis herpetiformis
	http://www.orpha.net/ORDO/Orphanet_602 Distal myopathy, Nonaka type
	http://www.orpha.net/ORDO/Orphanet_2841 Familial benign chronic pemphigus
	http://www.ebi.ac.uk/efo/EFO_0005676 Autoimmune Hepatitis
	http://www.ebi.ac.uk/efo/EFO_0009313 Linear IgA Dermatosis
	http://www.ebi.ac.uk/efo/EFO_0000540 immune system disease

lindenb / finddups.nf

Created March 4, 2020 13:51

workflow nextflow finding duplicated files and creating a bash script to replace the duplicate with a symbolic link

	params.directories="."
	params.headsize=100000
	params.extensions="bam bai"
	params.help=false
	params.extrafind=""
	params.lines = 1000
	params.publishDir="."

	def helpMessage() {
	log.info"""

lindenb / bam2cram.nf

Created March 4, 2020 08:22

BAM to CRAM workflow . bam cram reference fasta nextflow nf

	params.directories="."
	params.help=false
	params.references=""
	params.prefix=""
	params.publishDir="."
	params.extrafind=""

	references = file(params.references)

	def helpMessage() {

lindenb / fastq2ucram.nf

Last active February 29, 2020 18:58

fastq2ucram fastq to ucram nextflow cram bam fastq

	params.directories="."
	params.help=false
	params.center="Nantes"
	params.reference=""
	params.prefix=""
	params.publishDir="."

	def helpMessage() {
	log.info"""

lindenb / roh.nf

Created January 23, 2020 12:08

nextflow workflow for 'bcftools roh' . bioinformatics autozygosity vcf cnv

	params.prefix="output."
	params.vcf=""
	params.help=false
	params.rohopts=" --rec-rate 100 --skip-indels "
	params.pedigree = "NO_PED"

	def helpMessage() {
	log.info"""

	=========================================

lindenb / somalier.nf

Last active January 17, 2020 07:55

nextflow workflow for somalier #nextflow #workflow #somalier #relatedness #samples #bam

	params.prefix="output."
	params.bamlist=""
	params.sites="https://github.com/brentp/somalier/files/3412453/sites.hg19.vcf.gz"
	params.help=false
	params.pedigree="NO_FILE"

	def helpMessage() {
	log.info"""

	=========================================

lindenb / 20191221.callrnaseq.nf

Last active December 23, 2019 20:48

Calling RNASeq Encode

	gatk="/home/lindenb/packages/gatk/gatk-4.1.4.1/gatk"

	String jvarkit(String tool) {
	return "/home/lindenb/src/jvarkit-git/dist/"+tool+".jar";
	}
	reference=file(params.reference)

	process extractor {
	tag "script extracting bounds"
	cache 'lenient'

lindenb / merge_pdfs.bash

Created December 18, 2019 14:22

merging multiple pdfs using ghostview and recursion ( gs recursive recursif pdf)


	merger() {
	echo "merging \$1 and \$2" 1>&2
	ls -lah "\$1" "\$2" 1>&2
	gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile=jeter.pdf "\$1" "\$2"
	mv jeter.pdf "\$1"
	rm "\$2"
	}

lindenb / biostar.xslt

Created September 30, 2019 12:26

https://www.biostars.org/p/2867/ blast xslt xsl

	<?xml version='1.0' encoding="UTF-8" ?>
	<xsl:stylesheet
	xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
	version='1.0'
	>
	<xsl:output method="xml" encoding="UTF-8" indent="yes"/>

	<xsl:template match="*\|text()">
	<xsl:copy>
	<xsl:apply-templates select="*\|text()"/>

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