apeltzer
Large-scale & cloud computing in the life sciences @nf-core . My private account. @alex_peltzer@genomic.social
Boehringer IngelheimBiberach an der Riss, Germany
Pinned Repositories
action-nextflow
WIP / NOT WORKING YET: GitHub action for setting up Nextflow https://www.nextflow.io/
BWA-Mismatches
CircularMapper
A method to improve mappings on circular genomes, using the BWA mapper
DeDup
A merged read deduplication tool capable to perform merged read deduplication on single end data.
EAGER-CLI
The EAGER Command Line Component
EAGER-GUI
The EAGER Pipeline
eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
scrnaseq
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
smrnaseq
A small-RNA sequencing analysis pipeline
apeltzer's Repositories
apeltzer/DeDup
A merged read deduplication tool capable to perform merged read deduplication on single end data.
apeltzer/CircularMapper
A method to improve mappings on circular genomes, using the BWA mapper
apeltzer/ClipAndMerge
The Clip&Merge Method for paired end read merging and adapter clipping, quality trimming and other FastQ operations.
apeltzer/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
apeltzer/MTNucRatioCalculator
A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.
apeltzer/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
apeltzer/116117bot
A proof of concept bot, checking impfterminservice.de for available COVID-19 vaccination appointments.
apeltzer/apeltzer
apeltzer/bioconda-recipes
Conda recipes for the bioconda channel.
apeltzer/cbcltrimmer
A primitive tool to edit cbcl files
apeltzer/DamageProfiler
A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
apeltzer/depmap
Cancer Dependency Map package
apeltzer/docudigger
Website scraper for getting invoices automagically as pdf (useful for taxes or DMS)
apeltzer/facets
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
apeltzer/fusion-report
Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/
apeltzer/grocy
ERP beyond your fridge - grocy is a web-based self-hosted groceries & household management solution for your home
apeltzer/kleinanzeigen-bot
A dilligent command line tool to publish ads on ebay-kleinanzeigen.de
apeltzer/Mastodon-Bioinformatics
Most simple webapp to bulk follow bioinformatics accounts on Mastodon.
apeltzer/mirdata
Files needed for miRComb package
apeltzer/multi-package-containers
Testing building mulled containers for multi-requirement tools.
apeltzer/MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
apeltzer/nf-core-adr
Structurizr documentation of nf-core
apeltzer/r-mrgsolve-feedstock
A conda-smithy repository for r-mrgsolve.
apeltzer/r-nacho-feedstock
A conda-smithy repository for r-nacho.
apeltzer/SnpEff
apeltzer/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
apeltzer/starter-academic
🎓 Easily create a beautiful academic résumé or educational website using Hugo, GitHub, and Netlify
apeltzer/tldr
:books: Simplified and community-driven man pages
apeltzer/vaccipy
Automatische Terminbuchung für den Corona Impfterminservice.
apeltzer/whisperX
WhisperX: Automatic Speech Recognition with Word-level Timestamps (& Diarization)