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Pipeline codes for analyzing various genomics datasets based on MACS3
macs3-project / MAESTRO
Forked from liulab-dfci/MAESTROSingle-cell Transcriptome and Regulome Analysis Pipeline
A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data
Implementations of SIMD instruction sets for systems which don't natively support them.
A Github Action that executes jobs/commands on non-x86 cpu architectures (ARMv6, ARMv7, aarch64, s390x, ppc64le, riscv64) via QEMU
A python extension for quick access to bigWig and bigBed files
Tools to process and analyze deep sequencing data.
Episcanpy: Epigenomics Single Cell Analysis in Python
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…
Code examples of fast and simple k-mer counters for tutorial purposes
scikit-fusion: Data fusion via collective latent factor models
Convert between AnnData and SingleCellExperiment
Single-cell analysis in Python. Scales to >100M cells.
Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊
Single-cell Transcriptome and Regulome Analysis Pipeline
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data