AbeelLab/jaxkineticmodel

Building, simulating, and training systems biology models using JAX/Diffrax

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AbeelLab/simulated-dbtl

Language: Jupyter Notebook - Size: 16.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 1

AbeelLab/hat

Haplotype Assembly Tool

Language: Python - Size: 157 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 2

AbeelLab/safpred

Synteny-aware gene function prediction for bacteria using protein embeddings

Language: Python - Size: 17.4 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 4 - Forks: 2

AbeelLab/SAFPredDB

Bacterial synteny database

Language: Python - Size: 10.4 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

AbeelLab/SHIP

Language: Python - Size: 127 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 1

AbeelLab/RP2023_kirbeyi Fork of drkkrby/RP2023_kirbeyi

Research Project 2023-2024 Q2 - Kirbeyi

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AbeelLab/RP2023_Jarosz Fork of MJarosz22/RP2023_Jarosz

Size: 3.04 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

AbeelLab/RP2023_Alwani Fork of NeilAlwani/RP2023_Alwani

Contains the PPCA, VAE and CVAE model used for the research project. Aside from this there are separate folders for research documents and the dataset related to the project.

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AbeelLab/javaml

Java Machine Learning Library

Language: Java - Size: 15.7 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 40 - Forks: 20

AbeelLab/abaumannii-pangenome

Language: Python - Size: 8.79 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

AbeelLab/quanttb

QuantTB is a SNP based method to identify and quantify individual strains present in tuberculosis whole genome sequencing datasets.

Language: Python - Size: 140 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 5

AbeelLab/aneusim

A tool to generate synthetic aneuploid and polyploid genomes

Language: Python - Size: 42 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 0

AbeelLab/ptolemy

Language: Scala - Size: 2.48 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 10 - Forks: 2

AbeelLab/long-read-assembly-benchmark

Language: Python - Size: 7.68 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

AbeelLab/quetzal-old 📦

Multi-reference genome browser

Language: Java - Size: 2.89 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

AbeelLab/reports 📦

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AbeelLab/genometools

GenomeTools is a collection of algorithms to manipulate genomics related file format. The primary purpose is to convert file formats from one to another.

Language: Java - Size: 59.7 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 1

AbeelLab/ctag

Graph genome browser

Language: Java - Size: 362 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

AbeelLab/polytools

Language: Java - Size: 108 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 1

AbeelLab/vlpb-assembly-workshop

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AbeelLab/abeellab.github.io

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AbeelLab/integrated_bioinformatics

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AbeelLab/lorikeet

Digital spoligotyping of MTB strains from Illumina read data

Language: Scala - Size: 45.3 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 1

AbeelLab/Alpaca

Alpaca is a stand-alone method for identifying mosaic events in microbial genomes.

Language: Scala - Size: 1.42 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 0

AbeelLab/cs4255

Course material for the Algorithms for sequence-based bioinformatics course (CS4255) at TU Delft

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AbeelLab/atk

Abeel Toolkit is set of utility classes that are used in our other projects.

Language: Java - Size: 112 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 1

AbeelLab/redwood2

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AbeelLab/graphlift

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AbeelLab/parrot

Universal genotyping for Mycobacterium tuberculosis strains from WGS

Language: Scala - Size: 1.46 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

AbeelLab/peacock

peacock is a visualization library for generating vector graphics from (very) large phylogenies and many types of meta-data

Language: Scala - Size: 68 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

AbeelLab/GraphClean

Assembly graph cleaning through machine learning improves de novo long-read assembly

Language: Python - Size: 4.58 MB - Last synced at: 3 months ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 2

AbeelLab/course_bioinformatics1819

Course repository for Bioinformatics (NB2161) 2018-2019

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AbeelLab/phasm-benchmarks

Snakemake pipeline for the PHASM genome assembler

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AbeelLab/labdocuments

Documents supporting the lab

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AbeelLab/ultraqc

High-throughput *NA sequencing quality control

Language: Java - Size: 626 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

AbeelLab/phasm

Haplotype-aware de novo genome assembly for polyploid organisms from long read data

Language: Python - Size: 21 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 1

AbeelLab/bluejay

Language: Java - Size: 21 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 1

AbeelLab/prosom

ProSOM is a promoter prediction program based on unsupervised clustering of physical properties of DNA. The program can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences by using self-organizing maps.

Language: Java - Size: 16.1 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

AbeelLab/macaw

Macaw is a tool to lineage-type MTB samples and to identified strain mixes in WGS data sets.

Language: Scala - Size: 38.7 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 1

AbeelLab/Pedca

PEDCA is a ploidy estimation algorithm that infers copy number of the contigs submitted as input based on the read coverage that are aligned to them. It only requires as an input an alignment file in .bam or .sam format of a library or set of libraries aligned to a reference file of the contigs that will be estimated.

Language: Java - Size: 120 MB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

AbeelLab/kmertree

Approximate tree building with kmers

Language: Java - Size: 6.26 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

AbeelLab/nanopore-cenpk113-7d

Supplementary data for our CENPK113-7D assembly paper

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AbeelLab/AfterQC Fork of OpenGene/AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

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AbeelLab/reveal Fork of jasperlinthorst/reveal

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AbeelLab/parakeet

IS6110 discovery from NGS data

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AbeelLab/colldr

Rapid TB drug resistance determination from NGS data

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AbeelLab/hadeda

Language: Scala - Size: 22.4 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

AbeelLab/ono

Order and orient

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AbeelLab/emu

Emu is a tool that canonicalizes non-identical representations of large insertions and deletions (indels) and substitutions across multiple genome samples.

Language: Scala - Size: 20.8 MB - Last synced at: over 1 year ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0

AbeelLab/ara

Language: Java - Size: 38.1 MB - Last synced at: over 1 year ago - Pushed at: almost 9 years ago - Stars: 0 - Forks: 1

AbeelLab/pilon Fork of broadinstitute/pilon

Pilon is an automated genome assembly improvement and variant detection tool

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