Pinned Repositories
AlignQC
Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.
CIBERSORT
A shell to facilitate loading / running CIBERSORT software in structured environments
good-neighbors
Identify neighborhoods based on local cell populations.
GSVA
A command-line interface and python module for R's GSVA bioconductor package
hla-polysolver
Fork of the Polysolver project
IDP
Fork of the IDP hybrid-seq alignment -- Apache 2.0 licensed -- Copyright 2014 Kin Fai Au
IDP-fusion
IDP-fusion 20150212 release
omeify
py-seq-tools
Free python libraries for working with biological sequences, alignments, and formats
pythologist
Read and analyze exports of microscopy image data.
jason-weirather's Repositories
jason-weirather/pythologist
Read and analyze exports of microscopy image data.
jason-weirather/good-neighbors
Identify neighborhoods based on local cell populations.
jason-weirather/multiplex-if-simulator
Simulate multiplex IF data
jason-weirather/cio-mass-cytometry
jason-weirather/omeify
jason-weirather/tiff-inspector
A package for examining the structure and contents of the metadata contained within tiff files
jason-weirather/pythologist-reader
Reading functions to generate projects for storage and producing dataframes suitable for pythologist analysis
jason-weirather/ark-analysis
Integrated pipeline for multiplexed image analysis
jason-weirather/azure-vault-loader
A tool for loading secrets from azure key vault secrets onto remote machines holding proper credentials.
jason-weirather/bioformats2raw
Bio-Formats image file format to raw format converter
jason-weirather/comfyui-image-api
Host an API to execute ComfyUI Flux-dev image generation workflows
jason-weirather/deepcell-tf
Deep Learning Library for Single Cell Analysis
jason-weirather/fediverse-sandbox
Spin up multiple activitypub servers to test the fediverse
jason-weirather/gonk-diffusers-api
Python API for transforming text into vivid images using Stable Diffusion, with GPU support and concurrency control.
jason-weirather/jason-weirather.github.io
Make a cool portfolio repo
jason-weirather/kiosk-imageJ-plugin
An ImageJ Plugin for interacting with the DeepCell Kiosk
jason-weirather/ktistec
Single user ActivityPub (https://www.w3.org/TR/activitypub/) server.
jason-weirather/mibitracker-client
Python client for IONpath MIBItracker API, plus utility functions for working with MIBItiff images.
jason-weirather/ome-model
OME model (specification, code generator, implementation)
jason-weirather/ome-schema
A fork of the Open Microscopy Environment (OME) schema
jason-weirather/promptfoo
Test your prompts. Evaluate and compare LLM outputs, catch regressions, and improve prompt quality.
jason-weirather/pyppeteer
Headless chrome/chromium automation library (unofficial port of puppeteer)
jason-weirather/pythologist-image-utilities
Functions for working with image data in python
jason-weirather/pythologist-schemas
Check assumptions for input types prior to ingestion.
jason-weirather/pythologist-test-images
Images for use in unit tests etc
jason-weirather/raw2ometiff
Raw format to OME-TIFF converter
jason-weirather/snac-fork
A fork of snac2 - A simple, minimalistic ActivityPub instance
jason-weirather/wdl-pipelines
jason-weirather/yahoo_fin
Scrape stock price history from new (Spring 2017) Yahoo Finance layout
jason-weirather/zarr-python
An implementation of chunked, compressed, N-dimensional arrays for Python.