Mar111tiN
I started out as cancer researcher and now reach out into the world of data science
Berlin, Germany
Pinned Repositories
CNVascat
snakemake implementation of the ASCAT-Refphase CNV workflow
datadockers
collection of base docker images for datascience
filterbam
creates a set of filterbam files for use in IGV from mutation list and original (LARGE) bam files
FullStackOpen
Following the FullStackOpen tutorial on https://fullstackopen.com/
mawktools
collection of mawk tools for ultra-fast bioinformatic data processing
myCNV
CopyNumberVariation detection in WES data using coverage and heteroSNP
primertools
(optionally containerized) tools for creating primers, searching and indexing primers
somVarWES
full-fledged pipeline for detecting somatic variants in WES data
targetSeq
pipeline for mutation calling in unmatched deep-sequenced data
WorldMap
interactive Word Map using d3
Mar111tiN's Repositories
Mar111tiN/somVarWES
full-fledged pipeline for detecting somatic variants in WES data
Mar111tiN/myCNV
CopyNumberVariation detection in WES data using coverage and heteroSNP
Mar111tiN/primertools
(optionally containerized) tools for creating primers, searching and indexing primers
Mar111tiN/WorldMap
interactive Word Map using d3
Mar111tiN/datadockers
collection of base docker images for datascience
Mar111tiN/mawktools
collection of mawk tools for ultra-fast bioinformatic data processing
Mar111tiN/10xCX
Mar111tiN/bam2fastq
converts bam files into paired fastq files
Mar111tiN/biodockers
containers for bioinformatic research
Mar111tiN/cellrangersnake
snakemake pipeline for preprocessing 10x-NGS-data using cellranger
Mar111tiN/clarapi
Mar111tiN/CNVvalidation
workflow for validation of CNV results and subsequent VAF adjustment in SNV data
Mar111tiN/deepseqvali
pipeline for validation of known mutations using deep sequencing
Mar111tiN/digiwest
tools for working with Digiwest data
Mar111tiN/ebscore
Mar111tiN/HDRdetect
bioinformatic tool for the detection of false-positive mutations in bam-files caused by mapping artefacts
Mar111tiN/lumipy
code collection and tools for working with Luminex data
Mar111tiN/panelseq
little tool for creating sample sheets from a sequencing excel
Mar111tiN/projectsceleton
Sceleton project folder as a template to start work from
Mar111tiN/pubMap
force-directed graph for publication interaction
Mar111tiN/pyseq
Assortment of tools to work with sequencing data and panel design
Mar111tiN/PythonDataScienceHandbook
Mar111tiN/PythonMachineLearning
notebooks accompanying the PythonMachineLearning book by Sebastian Raschka
Mar111tiN/pytools
loose collection of python functions for bioinformatics
Mar111tiN/qpcRtools
utils for visualising and normalizing ddPCR and real-timePCR raw data
Mar111tiN/Rmut
R tools for filtering and visualizing filter lists from somvarWES pipeline
Mar111tiN/RNAseq
simple RNAseq pipeline based on snakemake workflow with extensive QC
Mar111tiN/sarekpipe
Mar111tiN/shorties
lose bundle of condensest manuals
Mar111tiN/WESbam
create realigned recalibrated (possibly UMI-filtered) bam files from WholeExomSeq data