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Lists (3)
Starred repositories
BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Integrative Python library for RNA Secondary Structure Analysis
The LinearDesign mRNA design software.
A comprehensive library for computational molecular biology
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
Fast-ish (and correct!) quantile normalization in Python.
Predicting dynamic cellular protein-RNA interactions using deep learning and in vivo RNA structure
Multiple RNA secondary structures prediction from high throughput RNA structure profiling data
bioinformatics visualization tools with pyviz/bokeh
A unified and modular interface to homology modelling software
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
C++ API & command-line toolkit for working with BAM data
Patchwork for matplotlib: A subplot manager for intuitive layouts in matplotlib, seaborn, and plotnine.
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Efficient target prediction incorporating accessibility of interaction sites
A dataset for training and benchmarking deep learning models for RNA structure prediction
Model-based inference of P-site offsets for ribosome footprints
Library for KEGG pathway enrichment analysis