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Pierre Lindenbaum lindenb

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lindenb / biostar9592523.sparql
Last active April 12, 2024 19:04 Can you suggest a protein that has two chainst but only 50 total number of atoms?
PREFIX xsd: <>
PREFIX wikibase: <>
PREFIX wdt: <>
PREFIX wd: <>
PREFIX vg: <>
PREFIX up: <>
PREFIX uniprotkb: <>
PREFIX uberon: <>
PREFIX taxon: <>
PREFIX sp: <>
lindenb / Makefile
Created April 4, 2024 10:59
Tool to Identify Gene, Regulatory Role, and Function at Integration Sites
all: $(OUTDIR)/database.rdf query.01.sparql
/path/to/pache-jena-4.8.0/bin/arq --data=$< --query=query.01.sparql
$(OUTDIR)/database.rdf: $(OUTDIR)/go.rdf $(OUTDIR)/gtf.rdf
mkdir -p $(dir $@)
lindenb / out.log
Created March 25, 2024 08:24
diff bind
> #### Occupancy Analysis ####
> png("Clustering_Occupancy.png", width= 840, height = 840)
> plot(DBsample, cexRow = 1.4, cexCol = 1.4)
null device
> write("DBA COUNT", stderr())
lindenb /
Last active February 19, 2024 12:18
compile R as library


I'm trying to compile #RStat as a static library with the -fPIC flag (so I can use it within #java #jni)


rm -rvf  "TMP/R-4.3.2" TMP/jeter.tar.gz
mkdir -p TMP/R-4.3.2/lib/
wget -O TMP/jeter.tar.gz ""
cd TMP && tar xfz jeter.tar.gz && rm jeter.tar.gz &&  cd R-4.3.2 && \
lindenb /
Last active March 23, 2024 20:33
Delete Tweets

I want to delete all my tweets without deleting my account.

This script deletes your tweets and repost from twitter without using the Twitter API, just by using the firefox javascript scratchpad.

Chage YOURNAME in the script below.

The script is quite slow but it works so far , I set some long timeout to let the DOM document to (re)load.

May be it could be much faster but I'm not a javascript guy.

lindenb / nextflow.log
Created October 19, 2023 17:11
nextflow cut&run. Nothing happens and .nextflow.log contains java stackTrace about aws.
Oct-19 19:04:09.799 [S3TransferManager-6] WARN c.a.i.InstanceMetadataServiceResourceFetcher - Fail to retrieve token
com.amazonaws.SdkClientException: Failed to connect to service endpoint:
at com.amazonaws.internal.EC2ResourceFetcher.doReadResource(
at com.amazonaws.internal.InstanceMetadataServiceResourceFetcher.getToken(
at com.amazonaws.internal.InstanceMetadataServiceResourceFetcher.readResource(
at com.amazonaws.internal.EC2ResourceFetcher.readResource(
at com.amazonaws.auth.InstanceMetadataServiceCredentialsFetcher.getCredentialsEndpoint(
at com.amazonaws.auth.InstanceMetadataServiceCredentialsFetcher.getCredentialsResponse(
at com.amazonaws.auth.BaseCredentialsFetcher.fetchCredentials(
at com.amazonaws.auth.BaseCre
lindenb /
Created September 11, 2023 07:01 Nextflow - How to pass the yml yaml format input file from an argument to channel as a list
workflow {
ch = Channel.fromPath(params.samples).
def yaml = new org.yaml.snakeyaml.Yaml();
def map = yaml.load(F);
return map.samples;
lindenb / bio-anchor.html
Created August 28, 2023 16:20
A first test with WebComponent, extending HTMLElement javascript bioinformatics
<bio-anchor build="hg38">rs25</bio-anchor> and
<bio-anchor build="hg38">ENSG00000005108</bio-anchor>
<bio-anchor build="hg38">chr1:1234-1235</bio-anchor>
<bio-anchor build="hg38">xxx</bio-anchor>
lindenb / Makefile
Created August 3, 2023 12:29
biostars9571322 Mafile based ngs worfklow for tutorial
# input is
# DATA/father.R1.fq.gz
# DATA/father.R2.fq.gz
# DATA/mother.R1.fq.gz
# DATA/mother.R2.fq.gz
# DATA/child.R1.fq.gz
# DATA/child.R2.fq.gz
define mapreads
lindenb /
Created July 3, 2023 11:46
matériel artistes art artist pen pencil paper


  • carbon pen platinium DP800S
  • aquarelle winsor & newton
  • pinceaux "Raphaël*
  • papier 250g Clairefontaine