Highly cited and useful papers related to machine learning, deep learning, AI, game theory, reinforcement learning

Genomics Extension for SQLite

The labyrinth king judges your gene models.

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

Fast and flexible ORF finder

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus.

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment

Deep learning infrastructure for genomics

Monet: An open-source Python package for analyzing scRNA-Seq data using PCA-based latent spaces

Statistical power studies for multi-omics experiments.

Awesome free machine learning and AI courses with video lectures.

PacBio BAM C++ library

Extensive de-novo TE Annotator

Ultrafast GPU-enabled QTL mapper

Coding Genome Reconstruction using Iso-Seq data

A collection of various deep learning architectures, models, and tips

A package which efficiently applies any function to a pandas dataframe or series in the fastest available manner

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Graph-based mapping of long sequences, noisy or HiFi.

De novo clustering of long transcript reads into genes

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

SUPPA: Fast quantification of splicing and differential splicing

Transcript assembly and quantification for RNA-Seq

De novo assembler for single molecule sequencing reads using repeat graphs

Genome assembly soft-masking using Red (REpeat Detector)

Open workflow definitions for genomic analysis from MGI at WUSM.