Grace Bisulfite's repositories
cgmaptools
toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR
FuChouMethyl
Methyl Pipeline
split_alignment
Seperate ma&fa source reads from aligned BAM using snpSplit tools
100-Days-Of-ML-Code
100-Days-Of-ML-Code中文版
BGI-Full-Length-RNA-Analysis-Pipeline
Full-Length RNA Analysis pipeline developted by BGI RD group.
bustools
Tools for working with BUS files
Cassiopeia
A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
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)
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.
haplotyped-methylome
Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
Longbow
PacBio library for at most 15 linked segements
MethHaplo
allele specific DNA methylation haplotype region
MethylNet
Modular framework for deep learning predictions on methylation data.
nanoNOMe
nanoNOMe (Nucleosome Occupancy and Methylome nanopore sequencing) Analysis
ngmlr
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
scATAC-benchmarking
Benchmarking computational single cell ATAC-seq methods
SCENIC
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
SparK_plot
Publication quality NGS track plotting
SUPPA
SUPPA2: Fast quantification of differential splicing
TFEA
Transcription Factor Enrichment Analysis
TOBIAS
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
workflows
Semi-automated Bash workflows for epigenomic analyses: RNA-seq, ChIP-seq, ATAC-seq, etc.