Pierre Lindenbaum

makefile2graph. Creates a graph of dependencies from GNU-Make; Output is a graphiz-dot file or a Gexf-XML file.

jvarkit. Java utilities for Bioinformatics

xslt-sandbox. My xslt sandbox

verticalize. Simple tool to verticalize text delimited files.

jsandbox. My java Sandbox

cclindenb. some C/C++ code....

magic. file command's magic pattern file for bioinformatics

jbwa. Java Bindings (JNI) for bwa

mod_bio. apache2 modules for bioinformatics.

samtools-utilities. Utilities for Samtools ( http://samtools.sourceforge.net/ )

j4make. java Makefile Graph parser

hts-rdf. Managing sequencing data with RDF

ngsxml. generating workflows with XML and XSLT

gazoduc-nf. Nextflow Pipelines

rbcf. R Bindings for htslib/bcf

newicktools. Misc tools for newick format

courses. Courses

gatk-ui. Graphical Interface for the Genome Analysis Toolkit (GATK)

jsvelocity. Processing structured data (json,yaml, tables, ...) with apache velocity

htsfuse. FUSE (Filesystem in Userspace) accessing remote files behind http. It was first designed for bioinformatics but can be used for general purpose.

bionode. node.js for bioinformatics . Contains a REST server for the UCSC

mw4bio. MediaWiki extenstions for Bioinformatics

xml-patch-make. XML patch allowing GNU make to output the workflow as XML

bioman. manual pages for the bioinformatician

x11hts. X11 related utilities for hts

igvfox. firefox addon : IGV (Integrative Genomics Viewer) control through mozilla Firefox

bcfparser. java parser for BCF2.2 format (Binary VCF format). The current HTSJDK only supports BCF2.1

nf-htsjdk. nextflow plugin with htsjdk

pubmedtrending. pubmed trending data

lindenb.github.com. GitHub Page

htsjni. Native java bindings for htseq

bcfselectgt. VCF/Bcf genotypes filtering using htslib

genprog. Genetic programming in C

keyvalueds. A C++ cmd-line based key-value datastore

bioudf. Mysql User defined functions for Bioinformatics

vizbam. BAM visualization

bioinformatics-career-survey. Results of the bioinformatics career survey 2008

semontology. Software Evaluation Metrics Ontology (SEMO)

variationtoolkit. Automatically exported from code.google.com/p/variationtoolkit

ccsandbox. some C++ programs

pivot. Pivot table for linux: wikipedia: pivot table is a data summarization tool found in data visualization programs such as spreadsheets or business intelligence software. Among other functions, a pivot-table can automatically sort, count total or give the average of the data stored in one table or spreadsheet. It displays the results in a second table (called a "pivot table") showing the summarized data.

splitfastq. split a pair of fastq files into a stream of interleaved fastq records.

ibddb. IBD database/query

Galaxy-XSD. Galaxy XML tool wrapper XSD

knime4bio. Automatically exported from code.google.com/p/knime4bio

htsguile. htslib + guile

lindenb. Config files for my GitHub profile.

bioinfograph. Learning bioinformatics

genmedsvcat.

samtools. Fork of samtools

awk-sandbox. Awk Scripts

cmd-utils. Linux command line utilities

cwl-workflows. Community maintained workflows & tools (with examples)

bdbutils. Utilities for berkeleyDB

greasemonkey. My Greasemonkey scripts

monmakeamoi. Patch for GNU make v 4.0 including new functions

mozgv. XUL/Mozilla genome viewer