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ChIP-seq analysis notes from Ming Tang
A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
An efficient CLI to extract sequences from the SRA
Build and publish crates with pyo3, cffi and uniffi bindings as well as rust binaries as python packages
Framework for interrogating transcription-factor motifs and their syntax/grammars from neural-network interpretations
A deep learning-based tool to identify splice variants
Minima is a one-size-fits-all Jekyll theme for writers.
CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
calculate transcription factor motif cosine similarity using gapped or ungapped k-mer scores
Evolutionary conservation of transcription factor binding sites
Tool for plotting sequencing data along genomic coordinates.
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Examples of single-cell genomic analysis accelerated with RAPIDS
An easy-to-use, flexible website template for labs.
Log shell-commands and used files. Snapshot executed scripts. Fully automatic.
Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
🤗 smolagents: a barebones library for agents that think in code.
A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor.
accurate prediction of promoter activity and variant effects from massive parallel reporter assays
Create, manage, and run Jupyter notebooks with their dependencies