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aviary
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public |
aviary - Metagenomics pipeline using long and short reads.
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2025-04-14 |
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smoothxg
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public |
Local reconstruction of variation graphs using partial order alignment.
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2025-04-14 |
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fusion-report
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public |
Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline.
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2025-04-14 |
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searchgui
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public |
User-friendly graphical tool for using proteomics identification search engines.
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2025-04-14 |
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odgi
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public |
An optimized dynamic genome/graph implementation.
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2025-04-14 |
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perl-test-file
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public |
test file attributes
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2025-04-14 |
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eskrim
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public |
ESKRIM: EStimate with K-mers the RIchness in a Microbiome
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2025-04-14 |
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floria
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public |
Floria is method for recovering strain-level haplotypes and clusters of reads from metagenomic short or long read sequencing data by haplotype phasing.
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2025-04-14 |
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r-geneexpressionfromgeo
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public |
A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.
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2025-04-13 |
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vcflib
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public |
Command-line tools for manipulating VCF files.
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2025-04-13 |
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srnamapper
|
public |
Mapping small RNA data to a genome.
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2025-04-13 |
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arborator
|
public |
Arborator: Simplifying operationalized pathogen surveillance and outbreak detection
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2025-04-13 |
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igv
|
public |
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics
data and annotations.
|
2025-04-13 |
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kmercamel
|
public |
KmerCamel🐫 - compressing k-mer sets using masked superstrings.
|
2025-04-13 |
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cenote-taker3
|
public |
Cenote-Taker 3: Discover and annotate the virome.
|
2025-04-13 |
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shiba2sashimi
|
public |
A utility for creating sashimi plot from Shiba output
|
2025-04-13 |
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solvebio
|
public |
The SolveBio Python client
|
2025-04-13 |
|
scanpy-cli
|
public |
CLI for Scanpy
|
2025-04-13 |
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picard-slim
|
public |
Java tools for working with NGS data in the BAM format.
|
2025-04-13 |
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picard
|
public |
Java tools for working with NGS data in the BAM format
|
2025-04-13 |
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snakemake-executor-plugin-slurm
|
public |
A Snakemake executor plugin for submitting jobs to a SLURM cluster.
|
2025-04-13 |
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reframed
|
public |
Metabolic modeling package.
|
2025-04-13 |
|
perl-math-bigint
|
public |
Arbitrary size floating point math package
|
2025-04-13 |
|
dysgu
|
public |
A collection of tools for calling structural variants using short or long reads
|
2025-04-13 |
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superintervals
|
public |
Rapid interval intersections
|
2025-04-13 |
|
bedops
|
public |
High-performance genomic feature operations.
|
2025-04-13 |
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bindash
|
public |
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop.
|
2025-04-13 |
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tmscoring
|
public |
Python implementation of the TMscore program.
|
2025-04-13 |
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reduce
|
public |
Reduce - tool for adding and correcting hydrogens in PDB files.
|
2025-04-13 |
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ampliconsuite
|
public |
An end-to-end wrapper for focal amplification analysis from whole-genome sequencing using AmpliconArchitect and associated tools.
|
2025-04-13 |
|
plothic
|
public |
Plot Whole genome Hi-C contact matrix heatmap.
|
2025-04-13 |
|
mimi
|
public |
Molecular Isotope Mass Identifier.
|
2025-04-13 |
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seqscreen
|
public |
SeqScreen was created to sensitively assign taxonomic classifications, functional annotations, and Functions of Sequences of Concern (FunSoCs) to single, short DNA sequences or open reading frames.
|
2025-04-13 |
|
metafun
|
public |
Custom package for metafun workflow management
|
2025-04-13 |
|
r-acidsinglecell
|
public |
Toolkit for single-cell RNA-seq analysis that extends the functionality of SingleCellExperiment.
|
2025-04-13 |
|
r-acidbase
|
public |
Low-level base functions imported by Acid Genomics packages.
|
2025-04-12 |
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whatshap
|
public |
Phase genomic variants using DNA sequencing reads (haplotype assembly).
|
2025-04-12 |
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screadcounts
|
public |
SCReadCounts is a computational tool for a cell-level assessment of the read counts bearing a particular nucleotide at genomic positions of interest from single cell RNA sequencing (scRNA-seq) data.
|
2025-04-11 |
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oarfish
|
public |
oarfish is a tool for fast, accurate and versatile transcript quantification from long-read RNA-seq data
|
2025-04-11 |
|
eider
|
public |
Command line bioinformatics tools for DuckDB.
|
2025-04-11 |
|
giatools
|
public |
Tools required for Galaxy Image Analysis
|
2025-04-11 |
|
lexicmap
|
public |
efficient sequence alignment against millions of prokaryotic genomes
|
2025-04-11 |
|
strobealign
|
public |
Align short reads using dynamic seed size with strobemers
|
2025-04-11 |
|
cvanmf
|
public |
Bi-cross validation of NMF and signature generation and analysis
|
2025-04-11 |
|
epicore
|
public |
Compute core epitopes from multiple overlapping peptides.
|
2025-04-11 |
|
architeuthis
|
public |
Tool to analyze and summarize data for Kraken.
|
2025-04-10 |
|
fasten
|
public |
Perform random operations on fastq files, using unix streaming. Secure your analysis with Fasten!
|
2025-04-10 |
|
pyjess
|
public |
Cython bindings and Python interface to JESS, a 3D template matching software.
|
2025-04-10 |
|
severus
|
public |
A tool for somatic structural variant calling using long reads
|
2025-04-10 |
|
picrust2
|
public |
PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
|
2025-04-10 |
