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alpha_vantage

A python wrapper for Alpha Vantage API for financial data.

archr

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

backtesting

:mag_right: :chart_with_upwards_trend: :snake: :moneybag: Backtest trading strategies in Python.

baysor

Bayesian Segmentation of Spatial Transcriptomics Data

cellbender

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

cellphonedb

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

clusterphobic

Utilities for simplifying interactions with cluster computing resources

cromsfer

Cromwell Output Transfer

cromwell-lsf-testing

Tests for configuring Cromwell with an LSF job scheduler and container-based workflows

docker-cellpose

Docker container with CellPose and Python utility scripts

docker-cellranger

Dockerized CellRanger multi application

docker-fiji

Docker container with Fiji and Python utility scripts

docker_tutorial

SCRI tutorial for workflow management using Docker

genesets

isabl-job-opt

mgatk

mgatk: mitochondrial genome analysis toolkit

nf-xenium

Nextflow workflow to process 10x Xenium spatial gene expression data

phenograph

Subpopulation detection in high-dimensional single-cell data

python-oslom-runner

An OSLOM Runner for Python.

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scing

SCING: Single-Cell pIpeliNe Garden (pronounced as "sing" /siŋ/)

scing-notebooks

A collection of Jupyter notebooks which automate the creation of input files for SCING pipelines

seacells

SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

stalign

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

tiff-utils

Utilities for interacting with TIFF files in Python

wdl-cellranger-gex

WDLized Cell Ranger GEX

wdl-hellomoon

SAIL tutorial to create workflow with WDL