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scoring-matrices
|
public |
Dependency free, Cython-compatible scoring matrices to use with biological sequences.
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2025-04-18 |
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dbcan
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public |
Standalone version of dbCAN annotation tool for automated CAZyme annotation.
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2025-04-18 |
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amulety
|
public |
Python package to create embeddings of BCR amino acid sequences.
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2025-04-18 |
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syri
|
public |
Synteny and rearrangement identifier between whole-genome assemblies.
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2025-04-18 |
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gfftk
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public |
GFFtk: genome annotation GFF3 tool kit
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2025-04-17 |
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sigprofilermatrixgenerator
|
public |
SigProfiler matrix generator tool.
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2025-04-17 |
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trgt
|
public |
Tandem repeat genotyping and visualization from PacBio HiFi data
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2025-04-17 |
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libcarna
|
public |
Real-time 3D visualization of biomedical data and beyond
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2025-04-17 |
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roadies
|
public |
Reference-free Orthology-free Alignment-free DIscordance aware Estimation of Species tree (ROADIES).
|
2025-04-16 |
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captus
|
public |
Captus: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data.
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2025-04-16 |
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r-ukbrapr
|
public |
R functions to use in the UK Biobank Research Analysis Platform (RAP)
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2025-04-16 |
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ncbi-stxtyper
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public |
StxTyper identifies and types Stx operons from assembled genomic sequence.
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2025-04-16 |
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primer3
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public |
Design PCR primers from DNA sequence. From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it.
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2025-04-16 |
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grz-cli
|
public |
Tool for validation, encryption and upload of MV submissions to GDCs.
|
2025-04-16 |
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annonars
|
public |
Genome annotation based on Rust and RocksDB.
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2025-04-16 |
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mehari
|
public |
VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust.
|
2025-04-16 |
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muat
|
public |
A package for Mutation Attention Tool
|
2025-04-16 |
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fastp
|
public |
A ultra-fast FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...).
|
2025-04-16 |
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atlas
|
public |
ATLAS: Analysis Tools for Ancient and Low-depth Samples
|
2025-04-16 |
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augustus
|
public |
AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
|
2025-04-16 |
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snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-04-16 |
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snakemake
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-04-16 |
|
tower-cli
|
public |
The Tower CLI an interface to Nextflow Tower via the CLI
|
2025-04-16 |
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panaln
|
public |
Indexing pangenome for read alignment.
|
2025-04-16 |
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cdskit
|
public |
CDSKIT processes protein-coding sequences.
|
2025-04-16 |
|
lastz
|
public |
LASTZ is a program for aligning DNA sequences, a pairwise aligner.
|
2025-04-16 |
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caspeak
|
public |
A pipeline for finding non-reference mobile element insertions
|
2025-04-16 |
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gcluster
|
public |
Gcluster is a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes
|
2025-04-16 |
|
pneumo-typer
|
public |
Pneumo-Typer is a high-throughput capsule genotype visualization tool with integrated serotype and sequence type prediction for Streptococcus pneumoniae
|
2025-04-16 |
|
instanovo
|
public |
InstaNovo enables diffusion-powered de novo peptide sequencing in large scale proteomics experiments.
|
2025-04-16 |
|
annotsv
|
public |
Annotation and Ranking of Structural Variation.
|
2025-04-16 |
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concoct
|
public |
Clustering cONtigs with COverage and ComposiTion
|
2025-04-16 |
|
dna_features_viewer
|
public |
Plot features from DNA sequences (e.g. Genbank) with Python.
|
2025-04-16 |
|
cdbtools
|
public |
CDB (Constant DataBase) indexing and retrieval tools for FASTA files
|
2025-04-16 |
|
postmaster
|
public |
Postmaster is a tool for annotating transcriptome alignments with posterior alignment probabilities derived from salmon quantifications.
|
2025-04-16 |
|
delly
|
public |
Structural variant discovery by integrated paired-end and split-read analysis
|
2025-04-16 |
|
ampd-up
|
public |
De novo antimicrobial peptide sequence generation with recurrent neural networks
|
2025-04-15 |
|
replidec
|
public |
Replication Cycle Decipher for Phages.
|
2025-04-15 |
|
r-classdiscovery
|
public |
Defines the classes used for "class discovery" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.
|
2025-04-15 |
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r-floral
|
public |
Log-ratio Lasso regression for continuous, binary, and survival outcomes with (longitudinal) compositional features. See Fei and others (2024) <doi:10.1016/j.crmeth.2024.100899>.
|
2025-04-15 |
|
gottcha2
|
public |
Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) v2.
|
2025-04-15 |
|
paraclu
|
public |
Paraclu finds clusters in data attached to sequences.
|
2025-04-15 |
|
sfld
|
public |
SFLD pre/post-processing
|
2025-04-15 |
|
augur
|
public |
Process pathogen genome data for the Nextstrain platform.
|
2025-04-15 |
|
buscolite
|
public |
buscolite: busco analysis for gene predictions.
|
2025-04-15 |
|
biscuit
|
public |
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data.
|
2025-04-15 |
|
raxml-ng
|
public |
RAxML Next Generation: faster, easier-to-use and more flexible
|
2025-04-15 |
|
ms2rescore
|
public |
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
|
2025-04-15 |
|
psm-utils
|
public |
Common utilities for parsing and handling peptide-spectrum matches and search engine results.
|
2025-04-15 |
|
cmat
|
public |
ClinVar Mapping and Annotation Toolkit
|
2025-04-15 |
