Neuropathology Lab at Institute for Medical Genetics and Pathology, University Hospital Basel, Switzerland's repositories
CNsummaryplots
Script to compute copy number summary plots from Illumina 450k/EPIC methaltion arrays
conumee-2
conumee adapted for EPIC v2 950K by mwsill
conumeeSummary
In this version of the conumee package an additional step for baseline-correction based on BAF of SNPs is included, which allows for automated scoring of copy number alterations for genomic segments.
gase-gasal2
GASE/BWA-MEM seed-extension accelerated with GASAL2 (adapted for ubuntu 18.04)
IlluminaHumanMethylationEPICanno.ilm10b5.hg38
forked version of Illumina Human Methylation EPIC annotation to use with IlluminaHumanMethylationEPICB5manifest and minfi
IlluminaHumanMethylationEPICv2manifest
fork of the EPIC v2 manifest from mwsill
methylseqscripts
Scripts to preprocess methylseq data into pseudo-array form.
minfi
Devel repository for minfi forked from mwsill
minknow_api
Forked from ONT's minknow_api with custom modifications
minknow_api-2
Protobuf and gRPC specifications for the MinKNOW API (Basel Pathology Modifications)
nanodip_dependencies
Dependencies for NaniDiP
npbtestrepo
for git testing only
IlluminaHumanMethylationEPICv2manifest_regenerate
forked from jokergoo
minknow_api-3
cloned from https://github.com/nanoporetech/minknow_api on 2023-09-06
mm2-gb
A versatile pairwise aligner for genomic and spliced nucleotide sequences
nanodip_dev
Development repostitory of NanoDiP
nvtop_2-0-3
AMD and NVIDIA GPUs htop like monitoring tool (version 2.0.3) tested with cuda_11.4.2_470.57.02_linux.run
pyPaSWAS_ubn1804
Program for DNA/RNA/protein sequence alignment, read mapping and trimming. Extended python version of PaSWAS, supporting OpenCL and CUDA devices. Adapted for Ubuntu 18.04 in 2022.
sesame_1_19_10
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
sesame_1_21_7
zip forked from zwdzwd
sesameData_1_21_7
zip forked from zwdzwd
SOAP3-dp-ifp
Soap-dp-3 fixed make error
unifiedilmnarrays
Unified loader for Illumina Infinium Human Methylation arrays: 450K, EPIC 850K v1 and EPIC v2
vnc4_setup_X86_64
shell scripts and configs for setting up vnc4 server on xUbuntu18.04