R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
GeneWalk identifies relevant gene functions for a biological context using network representation learning
KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph
Flexible analysis of high-content CRISPR screening
✂️ Pooled CRISPR screen optimization tool
Examples to get started with IBM Functional Genomics Platform
Robust and efficient analysis of single-cell perturbation studies
Analysis for "K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas" (Jessa et al, Nature Genetics, 2022)
TnSeq data processing workflow
A system for the integration and analysis of heterogeneous functional genomics data.
Continuous enrichment profiling for transcriptomes. Characterise how functional programmes are distributed across the expression gradient, with built-in significance testing for single samples. Great for non-model organisms, clinical isolates, and unreplicated datasets.
Documentation site for the Geneweaver project.
Laboratoare licență anul IV — Bioinformatica și Genomică Funcțională, cu focus pe ML, rețele și GenAI.
A curated list of regulatory genomics papers and resources.
A client library for the integration and analysis of heterogeneous functional genomics data.
RPuGB (Raeumliche Perturbations- und Gewebesimulations-Bibliothek) is a scientific Python library for spatial perturbation analysis, causal bystander decoupling, and in silico tissue simulation in functional genomics.
In-house scripts for data processing and analysis
Developed by Qiaoshan Lin in Yaowu Yuan Lab
Merge multiple peak calling experiments into consensus peaks and a sparse consensus by sample matrix (part of MUFFIN suite).
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