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clusty
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public |
Clusty is a tool for large-scale data clustering.
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2024-11-27 |
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kmer-db
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public |
Kmer-db is a fast and memory-efficient tool for estimating evolutionary distances.
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2024-11-27 |
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lz-ani
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public |
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes
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2024-11-27 |
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spatialleiden
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public |
Implementation of multiplex Leiden for analysis of spatial omics data.
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2024-11-27 |
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cojac
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public |
Command-line tools to analyse co-occurrence of mutations on amplicons.
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2024-11-27 |
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arvados-python-client
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public |
Python API for Arvados
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2024-11-26 |
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genera
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public |
Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
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2024-11-25 |
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agc
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public |
Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans).
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2024-11-25 |
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cobs
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public |
Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
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2024-11-25 |
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omamer
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public |
OMAmer - tree-driven and alignment-free protein assignment to sub-families
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2024-11-25 |
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biobb_vs
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public |
Biobb_vs is the Biobb module collection to perform virtual screening studies.
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2024-11-25 |
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damidseq_pipeline
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public |
An automated pipeline for processing DamID sequencing datasets.
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2024-11-25 |
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vgorient
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public |
Scripts for processing mitochondrial graphs.
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2024-11-25 |
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hmftools-sigs
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public |
Fits sample SNV counts to trinucleotide signature definitions.
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2024-11-25 |
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stranger
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public |
Annotate VCF files with STR variants with pathogenicity implications.
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2024-11-25 |
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straglr
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public |
Short-tandem repeat genotyping using long reads
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2024-11-25 |
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absense
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public |
abSENSE: a method to interpret undetected homologs
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2024-11-25 |
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clinker-py
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public |
Gene cluster comparison figure generator
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2024-11-25 |
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ashlar
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public |
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
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2024-11-25 |
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hifiadapterfilt
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public |
Convert .bam to .fastq and remove reads with remnant PacBio HiFi adapter sequences
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2024-11-25 |
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halfdeep
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public |
Automated detection of intervals covered at half depth by sequenced reads.
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2024-11-23 |
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scspectra
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public |
Supervised discovery of interpretable gene programs from single-cell data.
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2024-11-22 |
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meteor
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public |
Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems.
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2024-11-22 |
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panta
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public |
PanTA - pan-genome pipeline
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2024-11-22 |
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htsinfer
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public |
HTSinfer infers metadata from Illumina high throughput sequencing (HTS) data
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2024-11-22 |
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simug
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public |
A simple, flexible, and powerful tool to simulate genome sequences with pre-defined or random genomic variants.
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2024-11-22 |
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ega-cryptor
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public |
EGA Cryptor v2.0.0 is a tool designed to encrypt files compliant with the European Genome-phenome Archive (EGA)
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2024-11-22 |
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biobb_structure_utils
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public |
Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file.
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2024-11-21 |
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biobb_pytorch
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public |
biobb_pytorch is the Biobb module collection to create and train ML & DL models.
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2024-11-21 |
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pdivas
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public |
PDIVAS: Pathogenicity predictor of Deep-Intronic Variants causing Aberrant Splicing
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2024-11-21 |
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biobb_pmx
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public |
Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
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2024-11-21 |
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liana
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public |
LIANA+: a one-stop-shop framework for cell-cell communication
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2024-11-21 |
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hmftools-isofox
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public |
Isofox is a tool for counting fragment support for identifying and counting gene and transcript features using genome aligned RNASeq data in tumor samples.
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2024-11-21 |
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hmftools-lilac
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public |
LILAC is a WGS tool to determine HLA Class I types.
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2024-11-21 |
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hmftools-peach
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public |
Infer haplotypes for interpretation in a pharmacogenomic context
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2024-11-21 |
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r-dimsum
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public |
An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies
|
2024-11-20 |
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r-archr
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public |
This package is designed to streamline scATAC analyses in R.
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2024-11-20 |
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biobb_pdb_tools
|
public |
Biobb_pdb_tools is a swiss army knife for manipulating and editing PDB files.
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2024-11-20 |
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mess
|
public |
Snakemake pipeline for simulating shotgun metagenomic samples
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2024-11-20 |
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sprinter
|
public |
Single-cell Proliferation Rate Inference in Non-homogeneous Tumours through Evolutionary Routes (SPRINTER)
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2024-11-20 |
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biobb_model
|
public |
Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.
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2024-11-20 |
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biobb_gromacs
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public |
biobb_gromacs is the Biobb module collection to perform molecular dynamics simulations using the GROMACS MD suite.
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2024-11-20 |
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neptune-signature
|
public |
Neptune: Genomic Signature Discovery
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2024-11-20 |
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crabs
|
public |
Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a program to download and curate reference databases for eDNA metabarcoding analyses.
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2024-11-20 |
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svtopo
|
public |
Complex structural variant visualization for HiFi sequencing data: extraction tool
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2024-11-20 |
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search_ncbi
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public |
A package for searching and processing NCBI data
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2024-11-19 |
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mvip
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public |
MVP v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes and isolate genomes.
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2024-11-19 |
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hicstuff
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public |
General purpose stuff to generate and handle Hi-C data in its simplest form.
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2024-11-19 |
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hisat2-pipeline
|
public |
A pipeline to automatically run an RNA-seq analysis using HISAT2/Stringtie using default settings.
|
2024-11-19 |
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snpick
|
public |
A fast and memory-efficient tool for SNP extraction from genomic alignments.
|
2024-11-19 |
