a-thind

DESeq2

Differential expression of RNA-seq data using the Negative Binomial

Spring-Boot

condiments

Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

scran

Clone of the Bioconductor repository for the scran package.

tradeSeq

TRAjectory-based Differential Expression analysis for SEQuencing data

scDblFinder

Methods for detecting doublets in single-cell sequencing data

sc-type

monocle3

seurat-data

Dataset distribution for Seurat

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

cll-ibrutinib_time

tinyatlas

A tiny cell atlas for commonly sequenced organisms.

scrublet

Detect doublets in single-cell RNA-seq data

SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

seurat

R toolkit for single cell genomics

FinPipelines

This is a collection of my pipelines

Emma_scripts

single-cell-best-practices

https://www.sc-best-practices.org

MSC_Practicals

PaperGPT

Chat with research papers

20gene_signature

TCGAbiolinks

TCGAbiolinks

awesome-chatgpt-prompts

This repo includes ChatGPT prompt curation to use ChatGPT better.

surviplot

An R package for drawing survival curves with number-at-risk

SuperExactTest

Statistical testing and visualization of mult-set intersections

NumberGuessingGame

Taylor-Valeting-Website

Calculator