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100-days-of-ml-code

100 Days of ML Coding

atac-seq_quality_control_pipe

Atac-seq QC matrix

atac_seq_mm10

ATAC-seq data processing pipeline for mice datasets using mm10 genome

awesome-nanopore

A curated list of awesome nanopore analysis tools.

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

chip_seq

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

couplenmf

csbb-v3.0

CSBB - Computational Suite For Bioinformaticians and Biologists

cworld-dekker

perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)

deeplearningbook-chinese

Deep Learning Book Chinese Translation

dna-me-pipeline

DCC/DAC methylation pipeline source

dreg

Detecting Regulatory Elements using GRO-seq and PRO-seq

dropviz

Shiny app for visualization, exploration of mouse brain single cell gene expression

hic-bench

A set of pipelines for Hi-C and ChIP-Seq analysis.

integrate-neo

jogiles_atac

learnpython

以撸代码的形式学习Python

lincp21

Analysis scripts to accompany the paper "In vivo characterization of Linc-p21 reveals functional cis-regulatory DNA elements"

maftools

:cancer: Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

mcgn-ms

Multicellular gene network analysis identifies a macrophage-related gene signature predictive of therapeutic response and prognosis of gliomas

mel-ngs

ngs code for mel lab

metagene-maker

makes metagene plots for next-gen sequencing data over given regions

methylkit

R package for DNA methylation analysis

methylpy

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

nanom6a

nanonm

neo-epitome

Neo-Epitome: A Comprehensive Neoantigen/Neoeptipe prediction pipeline for NGS-guided cancer mutations and splicing variants detection coupling with MS data confirmation.

neoantigen-development

Collection of the bioinformatics tools for neoantigen

neoantigen_calling_pipeline

Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA