|
fast2q
|
public |
A Python3 program that counts sequence occurrences in FASTQ files.
|
2025-04-14 |
|
qcatch
|
public |
QCatch: Quality Control downstream of alevin-fry / simpleaf.
|
2025-04-14 |
|
latch
|
public |
The Latch python bioinformatics framework
|
2025-04-14 |
|
bioconductor-s4arrays
|
public |
Foundation of array-like containers in Bioconductor
|
2025-04-14 |
|
bioconductor-sparsearray
|
public |
High-performance sparse data representation and manipulation in R
|
2025-04-14 |
|
sr2silo
|
public |
Short-read to SILO format converter.
|
2025-04-14 |
|
ogtfinder
|
public |
OGTFinder is an optimal growth temperature prediction tool for prokaryotes using proteome-derived features.
|
2025-04-14 |
|
arvados-python-client
|
public |
Python API for Arvados
|
2025-04-14 |
|
ebi-eva-common-pyutils
|
public |
EBI EVA - Common Python Utilities.
|
2025-04-14 |
|
sniffles
|
public |
Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore).
|
2025-04-14 |
|
bioconductor-gosemsim
|
public |
GO-terms Semantic Similarity Measures
|
2025-04-14 |
|
pggb
|
public |
PanGenome Graph Building pipeline renders
|
2025-04-14 |
|
wfmash
|
public |
a pangenome-scale aligner
|
2025-04-14 |
|
methylartist
|
public |
Tools for parsing and plotting nanopore methylation data.
|
2025-04-14 |
|
bioconductor-rhtslib
|
public |
HTSlib high-throughput sequencing library as an R package
|
2025-04-14 |
|
bioconductor-rsamtools
|
public |
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
|
2025-04-14 |
|
ppanggolin
|
public |
PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph
|
2025-04-14 |
|
ltr_harvest_parallel
|
public |
Perl wrapper for parallel execution of LTR_harvest
|
2025-04-14 |
|
checkqc
|
public |
A simple program to parse Illumina NGS data and check it for quality criteria.
|
2025-04-14 |
|
libcifpp
|
public |
Library containing code to manipulate mmCIF and PDB files.
|
2025-04-14 |
|
carveme
|
public |
CarveMe: automated genome-scale metabolic model reconstruction
|
2025-04-14 |
|
gmap
|
public |
Genomic mapping and alignment program for mRNA and EST sequences.
|
2025-04-14 |
|
gsearch
|
public |
gsearch is an ultra-fast and scalable microbial genome search program based on MinHash-like metrics and graph-based approximate nearest neighbor search
|
2025-04-14 |
|
teloscope
|
public |
A telomere annotation tools for genome assemblies.
|
2025-04-14 |
|
cogent3
|
public |
COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems with 1000s of CPUs.
|
2025-04-14 |
|
gapmm2
|
public |
gapmm2: gapped alignment using minimap2.
|
2025-04-14 |
|
sawfish
|
public |
Structural variant discovery and genotyping from mapped PacBio HiFi data
|
2025-04-14 |
|
mach2
|
public |
Migration Analysis of Clonal Histories 2
|
2025-04-14 |
|
dmox
|
public |
Rust-based demultiplexing of haplotagging linked-read data.
|
2025-04-14 |
|
xtandem
|
public |
No Summary
|
2025-04-14 |
|
mypmfs_py
|
public |
Python package for mypmfs training (includes batch download from PDB).
|
2025-04-14 |
|
aviary
|
public |
aviary - Metagenomics pipeline using long and short reads.
|
2025-04-14 |
|
smoothxg
|
public |
Local reconstruction of variation graphs using partial order alignment.
|
2025-04-14 |
|
fusion-report
|
public |
Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline.
|
2025-04-14 |
|
searchgui
|
public |
User-friendly graphical tool for using proteomics identification search engines.
|
2025-04-14 |
|
odgi
|
public |
An optimized dynamic genome/graph implementation.
|
2025-04-14 |
|
perl-test-file
|
public |
test file attributes
|
2025-04-14 |
|
eskrim
|
public |
ESKRIM: EStimate with K-mers the RIchness in a Microbiome
|
2025-04-14 |
|
floria
|
public |
Floria is method for recovering strain-level haplotypes and clusters of reads from metagenomic short or long read sequencing data by haplotype phasing.
|
2025-04-14 |
|
r-geneexpressionfromgeo
|
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>.
|
2025-04-13 |
|
vcflib
|
public |
Command-line tools for manipulating VCF files.
|
2025-04-13 |
|
srnamapper
|
public |
Mapping small RNA data to a genome.
|
2025-04-13 |
|
arborator
|
public |
Arborator: Simplifying operationalized pathogen surveillance and outbreak detection
|
2025-04-13 |
|
igv
|
public |
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics
data and annotations.
|
2025-04-13 |
|
kmercamel
|
public |
KmerCamel🐫 - compressing k-mer sets using masked superstrings.
|
2025-04-13 |
|
cenote-taker3
|
public |
Cenote-Taker 3: Discover and annotate the virome.
|
2025-04-13 |
|
shiba2sashimi
|
public |
A utility for creating sashimi plot from Shiba output
|
2025-04-13 |
|
solvebio
|
public |
The SolveBio Python client
|
2025-04-13 |
|
oakvar
|
public |
OakVar - Genomic Variant Analysis Platform
|
2025-04-13 |
|
scanpy-cli
|
public |
CLI for Scanpy
|
2025-04-13 |
