Pinned Repositories
assembly_improvement
attrna.github.io
awesome-self-supervised-gnn
Papers about pretraining and self-supervised learning on Graph Neural Networks (GNN).
cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
codon_degeneracy
diploSHIC
docker-ngs-tools
A catalogue of docker images for NGS data analysis tools
easySFS
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
popGenMachineLearningExamples
simple examples of using supervised machine learning for population genetics inference
attrna's Repositories
attrna/attrna.github.io
attrna/awesome-self-supervised-gnn
Papers about pretraining and self-supervised learning on Graph Neural Networks (GNN).
attrna/codon_degeneracy
attrna/diploSHIC
attrna/easySFS
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
attrna/EvolveGCN
Code for EvolveGCN: Evolving Graph Convolutional Networks for Dynamic Graphs
attrna/gatk4-GenotypeGVCFs-nf
Joint calling of gVCF, following GATK4 Best Practices
attrna/gene_consensus_from_bam
attrna/genmap
GenMap - Fast and Exact Computation of Genome Mappability
attrna/GenomicConsensus
PacBio® variant and consensus caller
attrna/genomics_general
General tools for genomic analyses.
attrna/haplotypes
Visualizing evolution as a network of shared mutations
attrna/lecture_notes
attrna/mapping_pipeline
Mapping pipeline for data generated using Arima-HiC
attrna/msprime
A reimplementation of Hudson's classical ms simulator for modern data sets.
attrna/mutation_rate
Code and raw data files for my work on private polymorphism differences between populations.
attrna/nemADSQ
A repository containing pipelines for nematode genome assembly, decontamination, scaffolding, and QC
attrna/pepper
P.E.P.P.E.R.: Program for Evaluating Patterns in Pileups of Erroneous Reads
attrna/popgen-notes
Population genetics notes
attrna/pyABC
distributed, likelihood-free inference
attrna/pyslim
Tools for dealing with tree sequences coming to and from SLiM.
attrna/smcsmc
Demographic inference from whole genomes
attrna/stdpopsim
A library of standard population genetic models
attrna/tanagR
attrna/tests-as-linear
Common statistical tests are linear models (or: how to teach stats)
attrna/the-chaos-game
An R experiment to create fractals using the chaos game
attrna/tools
A collection of command-line tools I wrote to make various repetitive tasks more convenient
attrna/vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
attrna/wesanderson
A Wes Anderson color palette for R
attrna/worm2021_poster
Genome organization of Caenorhabditis brenneri