cbudjan

segment-anything

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.

pandas-ai

Chat with your database (SQL, CSV, pandas, polars, mongodb, noSQL, etc). PandasAI makes data analysis conversational using LLMs (GPT 3.5 / 4, Anthropic, VertexAI) and RAG.

obsidian-dataview

A data index and query language over Markdown files, for https://obsidian.md/.

agnoster-zsh-theme

A ZSH theme designed to disclose information contextually, with a powerline aesthetic

wesanderson

A Wes Anderson color palette for R

Obsidian-Templates

A repository containing templates and scripts for #Obsidian to support the #Zettelkasten method for note-taking.

BI-BE-CS-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

cellrank

CellRank: dynamics from multi-view single-cell data

micro-sam

Segment Anything for Microscopy

btrack

Bayesian multi-object tracking

CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Obsidian-Zettelkasten-Starter-Kit

A Starter Kit for Obsidian with all essential elements to build up your own Zettelkasten system.

chromap

Fast alignment and preprocessing of chromatin profiles

liana-py

LIANA+: an all-in-one framework for cell-cell communication

spectra

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

EmbedSeg

Code Implementation for EmbedSeg, an Instance Segmentation Method for Microscopy Images

moscot

Multi-omic single-cell optimal transport tools

bia-bob

BIA Bob is a Jupyter+LLM-based assistant for interacting with image data and for working on Bio-image Analysis tasks.

STACAS

R package for semi-supervised single-cell data integration

arboretum

Track and lineage visualization with btrack and Napari :evergreen_tree:

mubind

Learning motif contributions to cell transitions using sequence features and graphs.

qpcr

A python package to analyse qPCR data for single-use or high-throughput application

qupath-extension-cellsparse

QuPath extension for Cellsparse

deMULTIplex2

deMULTIplex2: robust sample demultiplexing for scRNA-seq

cross_system_integration

cellsparse-api

Cellsparse API

napari-biomag-annotator

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

Napari_Bioimage_Analysis

Image data and Python scripts for the course on Bioimage analysis with Napari

Cellos