Konrad Rokicki's repositories
batchspawner
Custom Spawner for Jupyterhub to start servers in batch scheduled systems
bigdataviewer-vistools
Helpers to use BigDataViewer as a quick visualization tool in other projects.
biocontainers
Bioinformatics containers
cellmap-hackathon-blog
CellMap hackathon blog
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
cobra
A Commander for modern Go CLI interactions
configs
Config files used to define parameters specific to compute environments at different Institutions
course22
The fast.ai course notebooks
n5-utils
simple standalone BigDataViewer for multiple N5 (or HDF5) datasets
n5-viewer
BigDataViewer-based tool for visualizing multichannel multiscale N5 datasets.
nextflow
A DSL for data-driven computational pipelines
nf-bigstitcher-demo
Demo of BigStitcher running in Spark using Nextflow
nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core-tools
Python package with helper tools for the nf-core community.
ome-zarr-image-analysis-nextflow
Basic example of using OME-Zarr in a Nextflow pipeline
open-data-registry
A registry of publicly available datasets on AWS
packr
The simple and easy way to embed static files into Go binaries.
quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
ray-janelia
Run Python Ray on the Janelia cluster
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
smaug
Multi-protocol bot
stitching-spark
Reconstruct big images from overlapping tiled images on a Spark cluster.
test-datasets
Test data to be used for automated testing with the nf-core pipelines
W_KR-i2k-IJNucleiSeg
BIAFLOWS workflow to segment clustered nuclei using a laplacian filter, thresholding and a binary watershed transform.