dariarom94

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

seurat

R toolkit for single cell genomics

prettyplotlib

Painlessly create beautiful matplotlib plots.

ML_course

EPFL Machine Learning Course, Fall 2024

gget

🧬 gget enables efficient querying of genomic reference databases

scRNAseq-analysis-notes

scRNAseq analysis notes from Ming Tang

nips14-ssl

Code for reproducing results of NIPS 2014 paper "Semi-Supervised Learning with Deep Generative Models"

atac-seq-pipeline

ENCODE ATAC-seq pipeline

dlcourse_ai

Материалы курса Deep Learning на пальцах

cellranger

10x Genomics Single Cell Analysis

Palantir

Single cell trajectory detection

DeepSequence

A generative latent variable model for biological sequence families.

scrublet

Detect doublets in single-cell RNA-seq data

10x-scATAC-2019

Publication Page for Satpathy*, Granja* et al 2019

stereoscope

Spatial mapping of cell types by integration of transcriptomics data

DOSNES

Doubly Stochastic Neighbor Embedding on Spheres

atacseq_pipeline

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data

gemBS

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

enrichment_analysis

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

AMULET

A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.

dea_limma

A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

toolkit

A toolkit for NGS analysis with Python

cemm.slurm.sm

CeMM's Snakemake SLURM cluster profile

spilterlize_integrate

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

DS32019

Materials for short course on Bayesian inference at the Data Science Summer School

RefFreeDMA

Reference Genome Independent Differential DNA Methylation Analysis

gapnet-pl

DNAmeth500species

Comparative analysis of DNA methylation across more than 500 animal species

atacseq_pipeline

BSF ATAC-seq pipeline