Trending repositories for topic genomics
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
Robs manual for the computational genomics and bioinformatics class.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
Robs manual for the computational genomics and bioinformatics class.
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Robs manual for the computational genomics and bioinformatics class.
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
MrBiomics - Modules & Recipes augment Bioinformatics for Multi-Omics Analyses at Scale
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Benchmarks for classification of genomic sequences
Official git repository for Biopython (originally converted from CVS)
MrBiomics - Modules & Recipes augment Bioinformatics for Multi-Omics Analyses at Scale
Robs manual for the computational genomics and bioinformatics class.
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Benchmarks for classification of genomic sequences
ClairS - a deep-learning method for long-read somatic small variant calling
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images - ICCV 2021
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Official git repository for Biopython (originally converted from CVS)
Complex structural variant visualization for HiFi sequencing data
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Robs manual for the computational genomics and bioinformatics class.
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Python library to facilitate genome assembly, annotation, and comparative genomics
MrBiomics - Modules & Recipes augment Bioinformatics for Multi-Omics Analyses at Scale
MrBiomics - Modules & Recipes augment Bioinformatics for Multi-Omics Analyses at Scale
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Robs manual for the computational genomics and bioinformatics class.
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
🌿: ABM & GIS for philological, archaeological, and anthropological data.
Benchmarks for classification of genomic sequences
ClairS - a deep-learning method for long-read somatic small variant calling
Official git repository for Biopython (originally converted from CVS)
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Scripts to download genomes from the NCBI FTP servers
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Python library to facilitate genome assembly, annotation, and comparative genomics
🌿: ABM & GIS for philological, archaeological, and anthropological data.
🌿: ABM & GIS for philological, archaeological, and anthropological data.
Portable solution to generate genome alignment chains using lastz
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Benchmarks for classification of genomic sequences
ClairS - a deep-learning method for long-read somatic small variant calling
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
Read specialized NGS formats as data frames in R, Python, and more.