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awesome-quant

A curated list of insanely awesome libraries, packages and resources for Quants (Quantitative Finance)

bokeh

Interactive Data Visualization in the browser, from Python

cb_sniffer

mutation(barcode) caller for 10x single cell data

concat-docker

An example of using Docker and Docker compose in our semi-standardised pipeline

cycif-clustering

Cell state calling docker app for cycif data

cycif_analysis_suite

A collection of tools for analysis of segmented single-cell cycif data.

datarail

Datarail's experimental design repository is a system for aiding the design, analyses, and visualization of high throughput dose response experiments.

deepdow

Portfolio optimization with deep learning.

drugresponse

Analysis of drug response based on cell staining

finquant

A program for financial portfolio management, analysis and optimisation.

histocat

Histology Topography Cytometry Analysis Toolbox

hms-lincs-tma

Analysis scripts for the tissue based Cycif data.

indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

indra_db

A Database-based knowledge back-end built on and for INDRA. The INDRA Database is a service that can be set up by any user with their own content and knowledge access. Our implementation of the database is the back-end to many of our projects, providing a vast and detailed knowledge base derived from many resources.

indra_pathway_map

intro-to-chipseq

Intro to ChIPseq using HPC

ipf-drug-discovery

kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

l1ktools

mongo

mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

models

Models and examples built with TensorFlow

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

nature_cancer_paper_2022

Code deposit for figures in manuscript

neuroc

Neuroconductor Content

pysashimi

Pure python scripts to make sashimi plots

python-ternary

:small_red_triangle: Ternary plotting library for python with matplotlib

qbrc-neoantigen-pipeline

Neoantigen calling pipeline with CSiN calculation embedded

qbrc-somatic-pipeline

Somatic mutation calling pipeline

qbrc_bulkrnaseqde

rna-seq-analysis

RNAseq analysis notes from Ming Tang