Pinned Repositories
sdg
Sequence Distance Graph framework: graph + reads + mapping + analysis
w2rap-contigger
An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.
mikado
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.
awesome-pipeline
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
fa2tree
Generate a PHYLIP file from different sized fasta files, the markers must have the same starting position but the end is not important
gpuMFEM
Point Based deformable models implementation, single core, multi-core (OpenMP) and GPU (CUDA)
ondaCUDA
Finite differences wave propagation on the GPU
pynb
ljyanesm's Repositories
ljyanesm/pynb
ljyanesm/awesome-pipeline
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
ljyanesm/ondaCUDA
Finite differences wave propagation on the GPU
ljyanesm/asub
A unified array job submitter for LSF, SGE/UGE and Slurm
ljyanesm/cheatsheets
My cheatsheets
ljyanesm/cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
ljyanesm/dkr-awscli-tf
ljyanesm/dotfiles
Based on lewagon's dotfiles! Thanks guys :)
ljyanesm/dtool-lookup-server
Given a dataset UUID returns a URI to where the dataset is stored
ljyanesm/ei-liftover
Repository to transfer gene models across (sub)genomes and check their coherence.
ljyanesm/gffread
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
ljyanesm/helm-charts
Helm Charts used to install Kiali resources.
ljyanesm/hera-workflows-feedstock
A conda-smithy repository for hera-workflows.
ljyanesm/homebrew-bio
:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
ljyanesm/IBSpy
Python library to identify Identical By State regions
ljyanesm/istio
Connect, secure, control, and observe services.
ljyanesm/k8s-device-plugin
NVIDIA device plugin for Kubernetes
ljyanesm/kseqcpp
A c++ port of @lh3 kseq.h
ljyanesm/openidconnect-rs
OpenID Connect Library for Rust
ljyanesm/pbrenderer
ljyanesm/pinfish
Tools to annotate genomes using long read transcriptomics data
ljyanesm/ranger
A Fast Implementation of Random Forests
ljyanesm/rdkit
The official sources for the RDKit library
ljyanesm/sc_seminar
github.io site for the sc_seminar
ljyanesm/seqtk
Toolkit for processing sequences in FASTA/Q formats
ljyanesm/spack
A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
ljyanesm/spaln
Genome mapping and spliced alignment of cDNA or amino acid sequences
ljyanesm/spliced_bam2gff
ljyanesm/stringtie
Transcript assembly and quantification for RNA-Seq
ljyanesm/wdl
Workflow Description Language - Specification and Implementations