Pinned Repositories
100-Days-Of-ML-Code
100 Days of ML Coding
2019-smORF
Scripts to identify small open reading frames using ribosome profiling data
af2complex
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
bio-pipeline
My collection of light bioinformatics analysis pipelines for specific tasks
DupGen_finder
A pipeline used to identify different modes of duplicated gene pairs
FunGAP
FunGAP: fungal Genome Annotation Pipeline
Liftoff
An accurate GFF3/GTF lift over pipeline
qvina
Accurately speed up AutoDock Vina
ribotricer
A tool for accurately detecting actively translating ORFs from Ribo-seq data
scripts-for-SSR-project
128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution
biogeeker's Repositories
biogeeker/AgRenSeq
biogeeker/ScanNet
biogeeker/SynNet-Pipeline
Workflow for Building Microsynteny Networks
biogeeker/hyphy
HyPhy: Hypothesis testing using Phylogenies
biogeeker/convert_gff_id
biogeeker/equidock_public
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
biogeeker/geta
biogeeker/cookiecutter-de_analysis_skeleton
Skeleton for new differential expression analysis project.
biogeeker/atac_analysis
For ATAC-seq analysis (papers, scripts and tools).
biogeeker/Finder
A fully automated gene annotator from RNA-Seq expression data
biogeeker/LJA
biogeeker/pbbioconda
PacBio Secondary Analysis Tools on Bioconda
biogeeker/Liftoff
An accurate GFF3/GTF lift over pipeline
biogeeker/ProteinGAN
biogeeker/GNN_PPI
Codes and models for the paper "Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction".
biogeeker/scripts-for-SSR-project
128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution
biogeeker/arcs
🌈Scaffold genome sequence assemblies using linked read sequencing data
biogeeker/genome_analysis
For genome assembly, annotation, and comparative genomics.
biogeeker/ntJoin
🔗Genome assembly scaffolder using minimizer graphs
biogeeker/rmats-turbo
biogeeker/TOPCONS2
Github for the TOPCONS2
biogeeker/AlignGraph2
Similar genome assisted reassembly pipeline for PacBio long reads
biogeeker/Bioinformatics-training-collection
A collection of resources for learning about tools and languages related to Bioinformatics
biogeeker/awesome-deepbio
A curated list of awesome deep learning applications in the field of computational biology
biogeeker/NAM-genomes
Detailed bioinformatics scripts and methods used in the NAM genome paper.
biogeeker/NextDenovo
Fast and accurate de novo assembler for long reads
biogeeker/chromosome_fusion
biogeeker/common_analyses
Repository of common bioinformatics scripts
biogeeker/bioinformatics_script
biogeeker/GenomeWorks
SDK for GPU accelerated genome assembly and analysis