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argo
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public |
Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping
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2025-01-13 |
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perl-graph
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public |
a Perl extension for keeping data partially sorted
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2025-01-13 |
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dnaapler
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public |
Reorients assembled microbial sequences
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2025-01-13 |
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annembed
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public |
annembed is an ultra-fast and scalable non-linear dimension reduction/embedding algorithm (similar to UMAP or t-SNE) for large-scale biological data
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2025-01-12 |
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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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2025-01-11 |
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sawfish
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public |
Structural variant discovery and genotyping from mapped PacBio HiFi data
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2025-01-10 |
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atlas
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public |
ATLAS: Analysis Tools for Ancient and Low-depth Samples
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2025-01-10 |
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biobb_mem
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public |
Biobb_mem is the Biobb module for membrane structure analysis.
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2025-01-10 |
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mzspeclib
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public |
HUPO-PSI Spectral library format
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2025-01-10 |
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cytotrace2-python
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public |
CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
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2025-01-10 |
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pyhmmer
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public |
Cython bindings and Python interface to HMMER3.
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2025-01-10 |
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gencove
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public |
Gencove is a high-throughput, cost-effective platform for genome sequencing and analysis. This command-line interface can be used to easily access the Gencove API.
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2025-01-10 |
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truvari
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public |
Structural variant comparison tool for VCFs
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2025-01-10 |
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metabolabpy
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public |
Python package to process 1D and 2D NMR spectroscopic data for metabolomics and tracer-based metabolism analysis.
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2025-01-10 |
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perl-experimental
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public |
Experimental features made easy
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2025-01-09 |
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prokbert
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public |
ProkBERT is a genomic language model specifically designed for microbiome applications. It leverages the power of machine learning to decipher complex microbial interactions, predict functionalities, and uncover novel patterns in extensive datasets. The ProkBERT model family, built on transfer learning and self-supervised methodologies, capitalizes on the abundant genomic data available.
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2025-01-09 |
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r-spacexr
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public |
Cell type identification and cell type-specific differential expression in spatial transcriptomics
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2025-01-09 |
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influx_si
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public |
Metabolic flux and concentration estimation based on stable isotope labeling
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2025-01-09 |
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glean-gene
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public |
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.
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2025-01-09 |
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star
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public |
An RNA-seq read aligner.
|
2025-01-09 |
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r-scroshi
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public |
scROSHI: robust supervised hierarchical identification of single cells
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2025-01-09 |
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caspeak
|
public |
A pipeline for finding non-reference mobile element insertions
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2025-01-09 |
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perl-uri-db
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public |
Database URIs
|
2025-01-09 |
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plothic
|
public |
Plot Whole genome Hi-C contact matrix heatmap
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2025-01-09 |
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spagrn
|
public |
A comprehensive tool to infer TF-centered, spatial gene regulatory networks for the spatially resolved transcriptomics (SRT) data.
|
2025-01-09 |
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relecov-tools
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public |
Tools for managing and processing of relecov data.
|
2025-01-09 |
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tir-learner
|
public |
An ensemble pipeline for terminal inverted repeat (TIR) transposable elements annotation.
|
2025-01-09 |
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snakemake-minimal
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-01-08 |
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snakemake
|
public |
A popular workflow management system aiming at full in-silico reproducibility.
|
2025-01-08 |
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gfaffix
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public |
GFAffix identifies and collapses walk-preserving shared affixes in variation graphs
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2025-01-08 |
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falco
|
public |
falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
|
2025-01-08 |
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sansa
|
public |
Structural variant annotation
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2025-01-08 |
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ibridges
|
public |
Package for accessing data and metadata on iRods servers.
|
2025-01-08 |
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r-crbhits
|
public |
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R.
|
2025-01-08 |
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ont-modkit
|
public |
A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data.
|
2025-01-08 |
|
bioconductor-pcaexplorer
|
public |
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
|
2025-01-08 |
|
bioconductor-genetonic
|
public |
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
|
2025-01-08 |
|
perl-config-general
|
public |
Generic Config Module
|
2025-01-08 |
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isorefiner
|
public |
A refinement tool to identify exon-intron structures of transcript (RNA) isoforms using long reads
|
2025-01-08 |
|
samrefiner
|
public |
A program for gathering variant information from a SAM formated files
|
2025-01-08 |
|
primalbedtools
|
public |
A collection of tools for working with primer.bed files
|
2025-01-08 |
|
hybpiper
|
public |
HybPiper is a suite of Python scripts/modules for targeted sequence capture.
|
2025-01-08 |
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simpleaf
|
public |
A rust framework to make using alevin-fry even simpler.
|
2025-01-07 |
|
gpatch
|
public |
Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference."
|
2025-01-07 |
|
parascopy
|
public |
Calling paralog-specific copy number and sequence variants in duplicated genes using short-read whole-genome sequencing.
|
2025-01-07 |
|
biscuit
|
public |
A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data.
|
2025-01-07 |
|
splitcode
|
public |
Flexible parsing, interpretation, and editing of technical sequences
|
2025-01-07 |
|
revbayes
|
public |
Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.
|
2025-01-07 |
|
suchtree
|
public |
A python library for doing fast, thread-safe computations on phylogenetic trees
|
2025-01-07 |
|
mashtree
|
public |
Create a tree using Mash distances
|
2025-01-07 |
