ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
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C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
- bioinformatics
- taxonomy
- cross-platform
- lineage
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
- single-cell
- scrna-seq
- scatac-seq
- deep-neural-networks
Predicting Cell Health with Morphological Profiles
- carpenter-lab
- morphological-profiling
- crispr
- cell-painting
A flexible Julia toolkit for high-dimensional cellular profiles
- julia
- morphological-analysis
- high-content-screening