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checkm-genome
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public |
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
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2024-09-23 |
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gsearch
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public |
gsearch is an ultra-fast and scalable microbial genome search program based on MinHash-like metrics and graph-based approximate nearest neighbor search
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2024-09-23 |
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bactopia
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public |
Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
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2024-09-22 |
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fastlin
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public |
fastlin, ultra-fast MTBC lineage typing
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2024-09-22 |
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perl-minion
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public |
Job queue
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2024-09-21 |
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bwa-aln-interactive
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public |
Version of the BWA aln read mapper for interactive alignment.
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2024-09-21 |
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recognizer
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public |
A tool for domain based annotation with the COG database
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2024-09-21 |
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eukfinder
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public |
Eukfinder is a tool for detecting eukaryotic sequences in metagenomic data.
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2024-09-21 |
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bactopia-qc
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public |
The methods used in Bactopia for read QC
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2024-09-21 |
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percolator
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public |
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
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2024-09-20 |
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phylodeep
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public |
Deep-learning parameter estimation and model selection from phylogenetic trees.
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2024-09-20 |
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fastq-screen
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public |
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
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2024-09-20 |
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seurat-scripts
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public |
A set of wrappers for individual components of the Seurat package.
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2024-09-20 |
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exomiser-rest-prioritiser
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public |
Exomiser prioritiser REST API
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2024-09-20 |
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wally
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public |
Visualization of aligned sequencing reads and genomic variants.
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2024-09-20 |
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busco_phylogenomics
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public |
Utility script to construct species phylogenies using BUSCO proteins.
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2024-09-20 |
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blast-legacy
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public |
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
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2024-09-20 |
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agat
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public |
Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
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2024-09-19 |
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fiji
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public |
Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
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2024-09-19 |
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peptides
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public |
Physicochemical properties, indices and descriptors for amino-acid sequences.
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2024-09-19 |
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emu
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public |
Emu is a relative abundance estimator for 16s genomic data.
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2024-09-19 |
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scarches
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public |
Transfer learning with Architecture Surgery on Single-cell data
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2024-09-19 |
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dfast_qc
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public |
DFAST_QC: Taxonomy and completeness check for prokaryotic genomes
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2024-09-19 |
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superdsm
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public |
SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.
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2024-09-19 |
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pydamage
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public |
Damage parameter estimation for ancient DNA
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2024-09-19 |
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methylartist
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public |
Tools for parsing and plotting nanopore methylation data
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2024-09-19 |
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seq-hasher
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public |
Compute hash digests for DNA sequences in a FASTA file, with support for circular permutations
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2024-09-19 |
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tr-trimmer
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public |
Identify and trim terminal repeats from sequences in FASTA files
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2024-09-19 |
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dicey
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public |
In-silico PCR and variant primer design
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2024-09-19 |
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abpoa
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public |
abPOA: fast SIMD-based partial order alignment using adaptive band
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2024-09-18 |
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pyabpoa
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public |
pyabpoa: SIMD-based partial order alignment using adaptive band
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2024-09-18 |
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igv-reports
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public |
Creates self-contained html pages for visual variant review with IGV (igv.js).
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2024-09-18 |
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r-wgcna
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public |
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
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2024-09-18 |
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pastml
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public |
Ancestral character reconstruction and visualisation for rooted phylogenetic trees.
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2024-09-18 |
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alignoth
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public |
A tool for creating alignment plots from bam files
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2024-09-18 |
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intarna
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public |
Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites
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2024-09-18 |
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ntjoin
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public |
Genome assembly scaffolder using minimizer graphs
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2024-09-18 |
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repeatmasker
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public |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
|
2024-09-17 |
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veryfasttree
|
public |
VeryFastTree -- speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies.
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2024-09-17 |
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genomepy
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public |
Install and use genomes & gene annotations the easy way!
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2024-09-17 |
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tracy
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public |
Basecalling, alignment, assembly and deconvolution of Sanger chromatogram trace files
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2024-09-17 |
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vcflib
|
public |
Command-line tools for manipulating VCF files.
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2024-09-17 |
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hylight
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public |
Strain aware assembly of low coverage metagenomes.
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2024-09-17 |
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transanno
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public |
accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies
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2024-09-17 |
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biophi
|
public |
BioPhi open-source antibody design platform.
|
2024-09-17 |
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fiji-omero_ij
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public |
ImageJ / Fiji plugin to visualize and manipulate both image data and metadata maintained at an OMERO server site.
|
2024-09-17 |
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mirtop
|
public |
Small RNA-seq annotation.
|
2024-09-17 |
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cellprofiler-core
|
public |
Dependency for CellProfiler v4.
|
2024-09-17 |
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snp-pileup
|
public |
Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets
|
2024-09-17 |
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microhapulator
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public |
Tools for empirical microhaplotype calling, forensic interpretation, and simulation.
|
2024-09-17 |
