wflynny

scamplers

A command-line utility to interact with a MongoDB designed for single cell data processing.

neuroglancer

WebGL-based viewer for volumetric data

dask_relabeling

A relabeling tool for tiled segmentation with Dask

pixi

Package management made easy

hvplot

A high-level plotting API for pandas, dask, xarray, and networkx built on HoloViews

bento-tools

A Python toolkit for subcellular analysis of spatial transcriptomics data

samui

A performant scientific image visualization system.

zellkonverter

Conversion between scRNA-seq objects

openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

nf-tenx

All 10x Genomics processing pipelines rolled into one containerized pipelines

simplecv

SimpleCV is a simple and elegant CV template written in Typst.

brilliant-CV

💼 another CV template for your job application, yet powered by Typst and more

typst

A new markup-based typesetting system that is powerful and easy to learn.

scbl-utils

A set of command-line utilities that facilitates data processing in the Single Cell Biology Lab at the Jackson Laboratory.

Nimbus

spatialdata-io

spatialdata_xenium_explorer

Converting any SpatialData object into files that can be open by the Xenium Explorer

loupeR

Convert Seurat objects to 10x Genomics Loupe files.

pyhamilton

Python for Hamilton liquid handling robots

seqspec

machine-readable file format for genomic library sequence and structure

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

campa

Conditional Autoencoders for Multiplexed Pixel Analysis

BPCells

Scaling Single Cell Analysis to Millions of Cells

pims

Python Image Sequence: Load video and sequential images in many formats with a simple, consistent interface.

metadata-schema

Repository to hold the MorPhiC metadata schema

Xenium_benchmarking

Code used to benchmark Xenium

UnMicst

UNet script, model, sample data

gos

A declarative library for Python designed to create interactive multi-scale visualizations of genomics and epigenomics data.

constclust

Consistent Clusters for scRNA-seq

holoviews

With Holoviews, your data visualizes itself.