alaminzju

DICE_COVID-19_GWAS_study

alaminzju.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

bpipe

Bpipe - a tool for running and managing bioinformatics pipelines

cellSNP

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

chat-gpt

ChatGPT conversation saving bookmark

CLIP-featurevis

code for reproducing some of the diagrams in the paper "Multimodal Neurons in Artificial Neural Networks"

Common_errors_NGS_data_analysis

FUMA-webapp

Source code of FUMA GWAS web application

GIST

Guiding-Image Spatial Transcriptomics

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

GWAS-softwares-and-tools.io

limix_qtl

MultiK

MultiK is a data-driven tool that objectively assesses the optimal number(s) of clusters based on the concept of consensus clustering via a multi-resolution perspective.

NG-Circos

NGS

Next-Gen Sequencing tools from the Horvath Lab

pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

r-source-1

Read-only mirror of R source code from https://svn.r-project.org/R/, updated hourly. See the build instructions on the wiki page.

scConsensus

An approach combining supervised and unsupervised clustering for cell type detection in single-cell RNA-seq data

scDeepCluster

scDeepCluster for Single Cell RNA-seq data

scPolyA-seq

https://pubmed.ncbi.nlm.nih.gov/36454750/

scRNA-seq

scTE

smartseq2

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.

snakemakeWorkflow

Bioinformatics-pipeline in snakemake.

SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

SnapHiC

SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data

TENET

TENET is a tool for reconstructing gene regulatory networks from pseudo-time ordered single-cell transcriptomic data.

TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

varCA

Use an ensemble of variant callers to call variants from ATAC-seq data

vsn-pipelines

A repository of pipelines for single-cell data in Nextflow DSL2