Pinned Repositories
gerlich_jupyter
Base container preinstalling all internally used NGS and image analysis tools.
gertils
general GERlich group uTILitieS
hicognition
A visual exploration and hypothesis testing tool for 3D genomics
hicognition_lib
HiCognition library and CLI tool
looptrace
Fork (from EMBL Gitlab) of the looptrace project: https://git.embl.de/grp-ellenberg/looptrace
ngs
A collections of functions to facilitate analysis of HiC data based on the cooler and cooltools interfaces.
scshic_analysis
Contains notebooks that analyse scsHi-C data and create the scsHi-C paper figures.
scshic_docker
Container with tools to analyse scsHi-C data.
scshic_pipeline
scsHi-C preprocessing Nextflow pipeline
spoc
gerlichlab's Repositories
gerlichlab/hicognition
A visual exploration and hypothesis testing tool for 3D genomics
gerlichlab/scshic_analysis
Contains notebooks that analyse scsHi-C data and create the scsHi-C paper figures.
gerlichlab/ngs
A collections of functions to facilitate analysis of HiC data based on the cooler and cooltools interfaces.
gerlichlab/scshic_pipeline
scsHi-C preprocessing Nextflow pipeline
gerlichlab/spoc
gerlichlab/looptrace
Fork (from EMBL Gitlab) of the looptrace project: https://git.embl.de/grp-ellenberg/looptrace
gerlichlab/gerlich_jupyter
Base container preinstalling all internally used NGS and image analysis tools.
gerlichlab/gertils
general GERlich group uTILitieS
gerlichlab/hicognition_lib
HiCognition library and CLI tool
gerlichlab/looptrace-loci-vis
Visualisation (in `napari`) of locus-specific spots from looptrace
gerlichlab/looptrace-napari
A `napari` plugin to facilitate interactive viewing of looptrace results
gerlichlab/nuclei-vis-napari
Visualisation (in `napari`) of nuclei from looptrace
gerlichlab/python-type-stubs
A set of type stubs for popular Python packages. These are works in progress from the Microsoft Python team and others, with the intent that they are contributed to typeshed or to the associated packages once sufficiently complete.
gerlichlab/python_club_2021
Python Club 2021
gerlichlab/spotfishing
Finding FISH spots
gerlichlab/higlassupload
Tool to preprocess data and upload it to a HiGlass instance
gerlichlab/schneider_et_al_Nature_2022
FIJI scripts used in Schneider et al. Nature (2022)
gerlichlab/scshic_docker
Container with tools to analyse scsHi-C data.
gerlichlab/triplet-exploration
dash app for exploring higher order triplet contacts
gerlichlab/Batty_et_al_EMBO.J_2023
Code used in Batty et al.
gerlichlab/dnascent-docker
Docker wrapper for DNAscent
gerlichlab/fguard
gerlichlab/gerlib
A library of general-purpose tools, typically for processing or analysis of data from a sequencing and/or imaging experiment
gerlichlab/gerlichlab
repo for github pages
gerlichlab/looptrace-regionals-vis
A `napari` plugin to facilitate interactive viewing of regional barcode spots from `looptrace`
gerlichlab/neubias_groupe4
Defragmentation Training School (NEUBIAS Academy) - Groupe 4 student
gerlichlab/python_club_seq_formats_I
Assignment for python club about sequencing formats
gerlichlab/sister-pore-c-docker
Main container for gerlichlab/sister-pore-c-snakemake
gerlichlab/sister-pore-c-snakemake
Extension of pore-c snakemake pipeline to include BrdU detection and sister chromatid discrimination
gerlichlab/tracebot
Clone of this project Ellenberg Lab (EMBL)