attrna Goto Github PK

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

evolvegcn

Code for EvolveGCN: Evolving Graph Convolutional Networks for Dynamic Graphs

evonet

funannotate

Eukaryotic Genome Annotation Pipeline

gatk4-genotypegvcfs-nf

Joint calling of gVCF, following GATK4 Best Practices

gene_consensus_from_bam

genmap

GenMap - Fast and Exact Computation of Genome Mappability

genomicconsensus

PacBio® variant and consensus caller

genomics_general

General tools for genomic analyses.

genotype-phenotype-notebooks

Continually updated data science Python notebooks: Deep learning (TensorFlow, Theano, Caffe), scikit-learn, Kaggle, big data (Spark, Hadoop MapReduce, HDFS), matplotlib, pandas, NumPy, SciPy, Python essentials, AWS, and various command lines.

go_enrichment

Transcripts annotation and GO enrichment Fisher tests

gt-dimred

Genotype dimension reduction research

haplotypes

Visualizing evolution as a network of shared mutations

hmmerctter

HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised Classification of Superfamily Protein Sequences with a reliable Cut-off Threshold

isoseq_sa3nup

Documentation and Developers Code Base for Iso-Seq SMRTAnalysis 3.x and beyond

ldhat_workflow

ldjump

R Package to Estimate Variable Recombination Rates using Population Genetic Data

lecture_notes

ltrsift

semi-automatic classification and postprocessing of LTR retrotransposons

mapping_pipeline

Mapping pipeline for data generated using Arima-HiC

msprime

A reimplementation of Hudson's classical ms simulator for modern data sets.

multipool

High-resolution genetic mapping for pooled sequencing.

mutation_rate

Code and raw data files for my work on private polymorphism differences between populations.