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squeegee
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public |
squeegee, de novo computational contamination detection tool for metagenomic samples
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2023-06-16 |
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tritimap
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public |
Triti-Map is a Snakemake-based pipeline for gene mapping in Triticeae.
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2023-06-16 |
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doubletd
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public |
doubletD is a method to detect doublets in single-cell DNA sequencing data
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2023-06-16 |
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gcen
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public |
GCEN: an easy-to-use toolkit for Gene Co-Expression Network analysis and lncRNAs annotation
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2023-06-16 |
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psytrans
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public |
psytrans.py - Parasite & Symbiont Transcriptome Separation
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2023-06-16 |
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zmwfilter
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public |
PacBio utility to filter reads on ZMW ID(s)
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2023-06-16 |
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extracthifi
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public |
PacBio utility to extract HiFi reads from CCS reads
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2023-06-16 |
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multitax
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public |
Python package to obtain, parse and explore biological taxonomies
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2023-06-16 |
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isoplot
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public |
Generate figures from Isocor output
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2023-06-16 |
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renet2
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public |
RENET2: High-Performance Full-text Gene-Disease Relation Extraction with Iterative Training Data Expansion
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2023-06-16 |
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dipcall
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public |
Dipcall is a reference-based variant calling pipeline for a pair of phased haplotype assemblies.
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2023-06-16 |
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python-codon-tables
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public |
Codon Usage Tables for Python, from kazusa.or.jp
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2023-06-16 |
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zpca
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public |
PCA analysis for genes or transcripts.
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2023-06-16 |
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ngmaster
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public |
In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST) and Neisseria gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR)
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2023-06-16 |
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lissero
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public |
In silico serotyping of Listeria monocytogenes
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2023-06-16 |
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ffindex-dbkit
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public |
Tools to create ffindex files
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2023-06-16 |
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alv
|
public |
A console-based sequence alignment viewer
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2023-06-16 |
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seidr
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public |
Community gene network inference and exploration toolkit
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2023-06-16 |
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gromacs_mpi
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public |
GROMACS is a versatile package to perform molecular dynamics.
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2023-06-16 |
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springsuite
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public |
The Spring Suite contains tools to predict and model protein-protein interactions from FASTA sequences and HHsearch threading results.
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2023-06-16 |
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scalop
|
public |
SCALOP - Sequence-based antibody Canonical LOoP structure annotation
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2023-06-16 |
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bacgwasim
|
public |
BacGWASim is a simulator for Bacterial Machine learning and Genome-wide Association studies.
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2023-06-16 |
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dadaist2-full
|
public |
Meta-package for Dadaist2 with full R packages, VSEARCH, CD-HIT and MultiQC
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2023-06-16 |
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troika-tb
|
public |
A pipeline implementing TB-Profiler for batch detection and reporting of anti-microbial resistance in TB for public health and clinical use.
|
2023-06-16 |
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godmd
|
public |
GOdMD Conformational Transitions with discrete Molecular Dynamics
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2023-06-16 |
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longestrunsubsequence
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public |
Implementation of a solver for the Longest Run Subsequence Problem. Given a sequence as input, compute a longest subsequence such that there is at most one run for every character.
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2023-06-16 |
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rodeo
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public |
RODEO evaluates one or many genes, characterizing a gene neighborhood based on the presence of profile hidden Markov models (pHMMs). Because RiPP precursor peptides are small and often evade annotation in sequence databases, RODEO can also manually translate small ORFs (open reading frames). A combination of support vector machine (SVM) learning and motif analysis can be used to scan unannotated intergenic regions for RiPP precursors.
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2023-06-16 |
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metaclassifier
|
public |
MetaClassifier is an integrated pipeline for classifying and quantifying DNA metabarcoding data into taxonomy groups
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2023-06-16 |
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leehom
|
public |
Maximum-likelihood adapter trimming and removal
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2023-06-16 |
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dms
|
public |
Comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level
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2023-06-16 |
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komb
|
public |
Characterizing metagenomes using K-Core decomposition
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2023-06-16 |
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gcta
|
public |
GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits.
|
2023-06-16 |
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haploview
|
public |
Haploview is designed to simplify and expedite the process of haplotype analysis by
providing a common interface to several tasks relating to such analyses.
|
2023-06-16 |
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calitas
|
public |
A CRISPR/Cas-aware ALigner for In silico off-TArget Search
|
2023-06-16 |
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machina
|
public |
Metastatic And Clonal History INtegrative Analysis
|
2023-06-16 |
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fmlrc2
|
public |
A rust implementation of fmlrc with faster run times.
|
2023-06-16 |
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mapula
|
public |
Calculation of alignment statistics
|
2023-06-16 |
|
flanker
|
public |
Gene-flank analysis tool
|
2023-06-16 |
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cassis
|
public |
Detection of genomic rearrangement breakpoints
|
2023-06-16 |
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beamspy
|
public |
BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python package)
|
2023-06-16 |
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aplanat
|
public |
Bokeh plotting API, with bio-focussed extras.
|
2023-06-16 |
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gplas
|
public |
gplas is a tool to bin plasmid-predicted contigs based on sequence composition, coverage and assembly graph information. It extends the possibility of accurately binning predicted plasmid contigs into several discrete plasmid components.
|
2023-06-16 |
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mitofinder
|
public |
Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.
|
2023-06-16 |
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mirnature
|
public |
MiRNAture improves on ideas from MIRfix and integrates it with homology search. miRNAture is specifically designed to identify and annotate metazoan miRNAs in a homology-based setting and is complementary to tools and pipelines that extract miRNA candidates from small RNA-seq data
|
2023-06-16 |
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ribolands
|
public |
Energy landscapes and folding kinetics of nucleic acids
|
2023-06-16 |
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crnsimulator
|
public |
Simulate chemical recation networks (CRNs) using ordinary differential equations (ODEs).
|
2023-06-16 |
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samap
|
public |
The SAMap algorithm
|
2023-06-16 |
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vulcan
|
public |
vulcan, map long reads and prosperđź––, a long read mapping pipeline that melds minimap2 and NGMLR
|
2023-06-16 |
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rnabridge-denovo
|
public |
A tool to construct the alignments of entire fragments given the alignments of paired-end reads.
|
2023-06-16 |
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jvarkit-wgscoverageplotter
|
public |
Whole genome BAM coverage plotter
|
2023-06-16 |
