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nf-core
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public |
Python package with helper tools for the nf-core community.
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2024-10-29 |
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geosketch
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public |
Geometry-preserving random sampling.
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2024-10-29 |
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pbsv
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public |
pbsv - PacBio structural variant (SV) calling and analysis tools
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2024-10-29 |
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pbtk
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public |
pbtk - PacBio BAM toolkit
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2024-10-29 |
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pbmarkdup
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public |
pbmarkdup - Mark duplicate reads from PacBio sequencing of an amplified library
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2024-10-29 |
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ppanggolin
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public |
PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph
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2024-10-29 |
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tides-ml
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public |
Tool for ORF-calling and ORF-classification using ML approaches.
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2024-10-29 |
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pbpigeon
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public |
PacBio transcript toolkit
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2024-10-29 |
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pgscatalog-utils
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public |
Utilities for working with PGS Catalog API and scoring files
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2024-10-29 |
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nordic
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public |
NORDic: a Network-Oriented package for the Repurposing of Drugs
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2024-10-29 |
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sainsc
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public |
Segmentation-free Analysis of In Situ Capture data.
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2024-10-29 |
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flippyr
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public |
This package is designed to align a PLINK fileset with a FASTA reference genome.
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2024-10-29 |
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massdash
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public |
MassDash is a streamlined DIA mass spec visualization, analysis, optimization, and rapid prototyping.
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2024-10-29 |
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prodigal-gv
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public |
A fork of Prodigal meant to improve gene calling for giant viruses
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2024-10-29 |
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chopper
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public |
A rust command line for filtering and trimming long reads.
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2024-10-29 |
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galaxy-files
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public |
The Galaxy file sources framework and default plugins.
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2024-10-29 |
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galaxy-data
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public |
The Galaxy models, datatype framework, and datatype implementations.
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2024-10-29 |
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galaxy-schema
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public |
The Galaxy API schema objects.
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2024-10-29 |
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pgscatalog.core
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public |
Core tools for working with polygenic scores (PGS) and the PGS Catalog
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2024-10-29 |
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corneto
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public |
CORNETO: A Unified Framework for Omics-Driven Network Inference
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2024-10-29 |
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nextclade
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public |
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
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2024-10-29 |
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galaxy-objectstore
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public |
The Galaxy object store framework and default implementations
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2024-10-29 |
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ucsc-bedgraphtobigwig
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public |
Convert a bedGraph file to bigWig format.
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2024-10-29 |
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ucsc-wigtobigwig
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public |
Convert ascii format wig file (in fixedStep, variableStep).
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2024-10-29 |
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kaptive
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public |
Reports information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.
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2024-10-28 |
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altamisa
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public |
Alternative Python API for accessing ISA-tab files.
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2024-10-28 |
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libgff
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public |
A simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase.
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2024-10-28 |
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seismic-rna
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public |
SEISMIC-RNA software by the Rouskin Lab
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2024-10-28 |
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dapcy
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public |
An sklearn implementation of discriminant analysis of principal components (DAPC) for population genetics.
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2024-10-28 |
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freyja
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public |
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
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2024-10-28 |
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merquryfk
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public |
MerquryFK replaces meryl with the FastK k-mer counter suite to considerably speed up analyses.
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2024-10-28 |
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lima
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public |
lima - The PacBio Barcode Demultiplexer
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2024-10-28 |
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fastk
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public |
FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.
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2024-10-28 |
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ucsc-pslcdnafilter
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public |
Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.
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2024-10-28 |
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pbaa
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public |
PacBio tool to cluster HiFi reads and generate high quality consensus sequences
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2024-10-28 |
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pbstarphase
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public |
A phase-aware pharmacogenomic diplotyper for PacBio sequencing data
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2024-10-28 |
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starfish
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public |
Standardized analysis pipeline for image-based transcriptomics.
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2024-10-28 |
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hlafreq
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public |
Download and combine HLA frequency data from multiple studies.
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2024-10-28 |
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sopa
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public |
Spatial-omics pipeline and analysis.
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2024-10-28 |
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staden_io_lib
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public |
Staden io_lib is a library of file reading and writing code e.g. for SAM/BAM/CRAM
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2024-10-28 |
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isoseq
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public |
Iso-Seq - Scalable De Novo Isoform Discovery
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2024-10-28 |
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pbskera
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public |
PacBio tool to split concatenated read designs
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2024-10-28 |
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masurca
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public |
MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.
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2024-10-28 |
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shortstack
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public |
ShortStack: Comprehensive annotation and quantification of small RNA genes
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2024-10-28 |
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kmer-jellyfish
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public |
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence
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2024-10-28 |
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dajin2
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public |
One-step genotyping tools for targeted long-read sequencing
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2024-10-28 |
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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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2024-10-28 |
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nanoqc
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public |
Create fastQC-like plots for Oxford Nanopore sequencing data.
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2024-10-28 |
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kinex
|
public |
Kinex infers causal kinases from phosphoproteomics data.
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2024-10-28 |
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d4binding
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public |
The C/C++ binding for the D4 file format.
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2024-10-28 |
