denvercal1234GitHub

Rphenoannoy

Optimised version of Rphenograph with annoy KNN - modified https://github.com/JinmiaoChenLab/Rphenograph

ProteomicsVisualization

This is a collection of minimal code to visualize various aspects of proteomics data.

cyCONDOR

Flow cytometry analysis workflow. The aim of this project if to provide an intuitive workflow for the analysis of high-dimensionality cytometry data in R.

cytofWorkflow

WholeSlideImageAnalysisWithQuPath

p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

STEGO.R

iDEA-Analysis

qupath-extension-stardist

QuPath extension to run StarDist nucleus detection

annotables

R data package for annotating/converting Gene IDs

Rade_et_al_tcell_2023

CU-CellSeg

Cell segmentation of multi-channel images

Chrysalis

Image processing software and Imaris Xtensions that expedite histo-cytometry analysis of 3D images and movies.

MAPS

Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications

BulkSignalR

BulkSignalR

scMulan

Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.

single-cell-transformer-papers

FigureOneLab

A running start for your computational biology portfolio.

Network-Analysis-Made-Simple

An introduction to network analysis and applied graph theory using Python and NetworkX

SingleRBook

The package wrapping the book, for deployment via the Bioconductor build system.

superheat

An r package for generating beautiful and customizable heatmaps

cell2sentence-ft

Cell2Sentence turns scRNA-seq data into text for LLM training.

scBubbletree

scBubbletree: quantitative tool for visual exploration of scRNA-seq data

qupath

QuPath - Bioimage analysis & digital pathology

FlexDotPlot

R package for Flexible dot plots

Covid-Tonsil

Robust, persistent adaptive immune responses to SARS-CoV-2 in oropharyngeal lymphoid tissue in children

ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

RF-PHATE

Official RF-PHATE repository.

RF-PHATE

Supervised visualization of high-dimensional data using random forests

compbio_tutorials