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100-days-of-ml-code

100-Days-Of-ML-Code中文版

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

bgi-full-length-rna-analysis-pipeline

Full-Length RNA Analysis pipeline developted by BGI RD group.

biocintegrativecancervis

bioinformatics-training

Bioinformatics training resources

bis-tools

A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )

bustools

Tools for working with BUS files

cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

cfdna

Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA

cgatpipelines

Collection of CGAT NGS Pipelines

cgmaptools

toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR

cistopic

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

cottonmnase-seq

Data analysis

dmrichr

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

dss

epigen_rcodes

fastqp

Simple FASTQ quality assessment using Python

fuchoumethyl

Methyl Pipeline

genrich

Detecting sites of genomic enrichment

handson-ml2

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.

hans.github.io

haplotyped-methylome

Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation

hla-la

Fast HLA type inference from whole-genome data

hmmratac

HMMRATAC peak caller for ATAC-seq data

improse

imPROSE - Integrated Methods for Prediction of Super-Enhancers

isoseq3

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

isoseq3_test

A simple test report for isoSeq3 of PacificBiosciences

lily

Detection of super-enhancers in cancer data

longbow

PacBio library for at most 15 linked segements

machine-learning-practice