cbudjan
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Finding gene expression states in scRNA-seq data
The package mixhvg uses mixture of highly variable gene selection methods to improve gene selection.
A collection of 50+ trajectory inference methods within a common interface 📥📤
scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions
An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code.
Open source Python library for building bioimage analysis pipelines
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
A python package to analyse qPCR data for single-use or high-throughput application
LIANA+: an all-in-one framework for cell-cell communication
deMULTIplex2: robust sample demultiplexing for scRNA-seq
Track and lineage visualization with btrack and Napari 🌲
The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
Segment Anything for Microscopy
BIA Bob is a Jupyter+LLM-based assistant for interacting with image data and for working on Bio-image Analysis tasks.
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Fast alignment and preprocessing of chromatin profiles
A data index and query language over Markdown files, for https://obsidian.md/.
A repository containing templates and scripts for #Obsidian to support the #Zettelkasten method for note-taking.
A Starter Kit for Obsidian with all essential elements to build up your own Zettelkasten system.