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varfish-server-worker
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public |
Rust-based tool for the heavy lifting in varfish-server.
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2024-08-16 |
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metabinner
|
public |
Ensemble binning method to recover individual genomes from complex microbial communities
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2024-08-16 |
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pyrodigal-gv
|
public |
A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.
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2024-08-15 |
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roadies
|
public |
Reference-free Orthology-free Alignment-free DIscordance aware Estimation of Species tree (ROADIES)
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2024-08-15 |
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pia
|
public |
PIA is a toolbox for MS based protein inference and identification analysis.
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2024-08-14 |
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snakemake-executor-plugin-googlebatch
|
public |
Snakemake executor plugin for Google Batch
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2024-08-14 |
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scar
|
public |
scAR (single-cell Ambient Remover) is a deep learning model for ambient signal removal in droplet-based single cell omicsis.
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2024-08-14 |
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pymochi
|
public |
Neural networks to quantify energies, energetic couplings, epistasis and allostery from deep mutational scanning data
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2024-08-14 |
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snakemake-storage-plugin-s3
|
public |
A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)
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2024-08-14 |
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singlem
|
public |
SingleM is a tool for profiling shotgun metagenomes. It has a particular strength in detecting microbial lineages which are not in reference databases. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, and lineage-targeted MAG recovery.
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2024-08-14 |
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cellbender
|
public |
A software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data
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2024-08-13 |
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tcdemux
|
public |
Demultiplex files and prepare reads for the target capture analysis pipeline.
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2024-08-13 |
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pdbx
|
public |
pdbx is a parser module in python for structures of the protein data bank in the mmcif format
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2024-08-13 |
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phyloaln
|
public |
PhyloAln: a reference-based multiple sequence alignment tool for phylogeny
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2024-08-13 |
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hairsplitter
|
public |
Recovers collapsed haplotypes from a draft assembly and long reads
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2024-08-12 |
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cryptkeeper
|
public |
A negative design tool for predicting and visualizing undesired gene expression
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2024-08-12 |
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phylofisher
|
public |
A package for the creation, analysis, and visualization of eukaryotic phylogenomic datasets.
|
2024-08-12 |
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treetime
|
public |
Maximum-Likelihood dating and ancestral inference for phylogenetic trees
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2024-08-11 |
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poolsnp
|
public |
PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.
|
2024-08-10 |
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pyani
|
public |
pyani provides a package and script for calculation of genome-scale average nucleotide identity.
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2024-08-09 |
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dingii
|
public |
Computing the Rearrangement Distance of Natural Genomes.
|
2024-08-09 |
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resfinder
|
public |
ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.
|
2024-08-09 |
|
rhotermpredict
|
public |
RhoTermPredict (Barrick Lab Fork)
|
2024-08-09 |
|
promotercalculator
|
public |
Promoter-Calculator (Barrick Lab Fork)
|
2024-08-09 |
|
fraposa-pgsc
|
public |
Tools to perform ancestry projection to a reference dataset within the calculator pipeline (pgsc_calc)
|
2024-08-08 |
|
cgpbigwig
|
public |
BigWig manpulation tools using libBigWig and htslib
|
2024-08-08 |
|
monsda
|
public |
MONSDA, Modular Organizer of Nextflow and Snakemake driven HTS Data Analysis
|
2024-08-08 |
|
sonicparanoid
|
public |
SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models
|
2024-08-07 |
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hybkit
|
public |
Hybkit toolkit and Python3 API chimeric genomic data analysis from proximity ligation methods.
|
2024-08-07 |
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bcgtree
|
public |
Automatized phylogenetic tree building from bacterial core genomes
|
2024-08-07 |
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bamdash
|
public |
Aggregate pathogen NGS results into an interactive plot
|
2024-08-07 |
|
pybdei
|
public |
Maximum likelihood estimation of Birth-Death Exposed-Infectious (BDEI) epidemiological model parameters from phylogenetic trees.
|
2024-08-07 |
|
snakemake-storage-plugin-azure
|
public |
A Snakemake storage plugin to read and write from Azure Blob Storage
|
2024-08-06 |
|
phylodeep_data_bdss
|
public |
Package containing data for the phylodeep package.
|
2024-08-06 |
|
chewbbaca
|
public |
A complete suite for gene-by-gene schema creation and strain identification.
|
2024-08-06 |
|
tracegroomer
|
public |
Format and normalise tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet analysis.
|
2024-08-06 |
|
cospar
|
public |
A toolkit for dynamic inference of cell fate by integrating state and lineage information.
|
2024-08-06 |
|
pytaxonkit
|
public |
Python bindings for the TaxonKit library.
|
2024-08-06 |
|
kin
|
public |
A tool to estimate pairwise relatedness from ancient DNA, taking in account contamination, ROH, ascertainment bias.
|
2024-08-06 |
|
phylodeep_data_bdei
|
public |
Package containing data for the phylodeep package.
|
2024-08-06 |
|
phylodeep_data_bd
|
public |
Package containing data for the phylodeep package.
|
2024-08-06 |
|
pbptyper
|
public |
In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
|
2024-08-06 |
|
cite-seq-count
|
public |
A python package to map reads from CITE-seq or hashing data for single cell experiments.
|
2024-08-05 |
|
bam-readcount
|
public |
bam-readcount generates metrics at single nucleotide positions.
|
2024-08-05 |
|
snapgene-reader
|
public |
Convert Snapgene *.dna files dict/json/biopython.
|
2024-08-02 |
|
pmultiqc
|
public |
Python package for quality control of proteomics datasets, based on multiqc package
|
2024-08-02 |
|
genewalk
|
public |
Determine gene function based on network embeddings.
|
2024-08-02 |
|
carveme
|
public |
CarveMe: automated genome-scale metabolic model reconstruction
|
2024-08-02 |
|
reframed
|
public |
Metabolic modeling package.
|
2024-08-02 |
|
ncbi-fcs-gx
|
public |
The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.
|
2024-08-01 |
