neuropathbasel
Neuropathology diagnostics and development team at University Hospital Basel, Switzerland. We maintain a publicly accessible platform (www.epidip.org).
University Hospital BaselSchönbeinstrasse 40, CH-4031 Basel
Pinned 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.
epidip
Epigenomic Digital Pathology - EpiDiP - explore human neoplastic and non-neoplastic epigenomes
gpumap
GPU-Parallelized UMAP
minknow_api
Forked from ONT's minknow_api with custom modifications
nanodip
Nanopore Digital Pathology - NanoDiP, the Nanopore companion of EpiDiP
nanodip_dependencies
Dependencies for NaniDiP
nanodip_dev
Development repostitory of NanoDiP
X86_64_MinKNOW_GUI_4.3.26_install_script
neuropathbasel's Repositories
neuropathbasel/nanodip
Nanopore Digital Pathology - NanoDiP, the Nanopore companion of EpiDiP
neuropathbasel/gpumap
GPU-Parallelized UMAP
neuropathbasel/epidip
Epigenomic Digital Pathology - EpiDiP - explore human neoplastic and non-neoplastic epigenomes
neuropathbasel/minknow_api
Forked from ONT's minknow_api with custom modifications
neuropathbasel/nanodip_dependencies
Dependencies for NaniDiP
neuropathbasel/nanodip_dev
Development repostitory of NanoDiP
neuropathbasel/X86_64_MinKNOW_GUI_4.3.26_install_script
neuropathbasel/CNsummaryplots
Script to compute copy number summary plots from Illumina 450k/EPIC methaltion arrays
neuropathbasel/conumee-2
conumee adapted for EPIC v2 950K by mwsill
neuropathbasel/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.
neuropathbasel/gase-gasal2
GASE/BWA-MEM seed-extension accelerated with GASAL2 (adapted for ubuntu 18.04)
neuropathbasel/IlluminaHumanMethylationEPICanno.ilm10b5.hg38
forked version of Illumina Human Methylation EPIC annotation to use with IlluminaHumanMethylationEPICB5manifest and minfi
neuropathbasel/IlluminaHumanMethylationEPICv2anno.20a1.hg38
neuropathbasel/IlluminaHumanMethylationEPICv2manifest
fork of the EPIC v2 manifest from mwsill
neuropathbasel/methylseqscripts
Scripts to preprocess methylseq data into pseudo-array form.
neuropathbasel/minfi
Devel repository for minfi forked from mwsill
neuropathbasel/minknow_api-2
Protobuf and gRPC specifications for the MinKNOW API (Basel Pathology Modifications)
neuropathbasel/npbtestrepo
for git testing only
neuropathbasel/IlluminaHumanMethylationEPICv2manifest_regenerate
forked from jokergoo
neuropathbasel/minknow_api-3
cloned from https://github.com/nanoporetech/minknow_api on 2023-09-06
neuropathbasel/mm2-gb
A versatile pairwise aligner for genomic and spliced nucleotide sequences
neuropathbasel/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
neuropathbasel/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.
neuropathbasel/sesame_1_19_10
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
neuropathbasel/sesame_1_21_7
zip forked from zwdzwd
neuropathbasel/sesameData_1_21_7
zip forked from zwdzwd
neuropathbasel/SOAP3-dp-ifp
Soap-dp-3 fixed make error
neuropathbasel/unifiedilmnarrays
Unified loader for Illumina Infinium Human Methylation arrays: 450K, EPIC 850K v1 and EPIC v2
neuropathbasel/upuntu
Manual updater script for ubuntu 18 and 20
neuropathbasel/vnc4_setup_X86_64
shell scripts and configs for setting up vnc4 server on xUbuntu18.04