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flippyr
|
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
|
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
|
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
|
public |
A rust command line for filtering and trimming long reads.
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2024-10-29 |
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galaxy-files
|
public |
The Galaxy file sources framework and default plugins.
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2024-10-29 |
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galaxy-data
|
public |
The Galaxy models, datatype framework, and datatype implementations.
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2024-10-29 |
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galaxy-schema
|
public |
The Galaxy API schema objects.
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2024-10-29 |
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pgscatalog.core
|
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
|
public |
CORNETO: A Unified Framework for Omics-Driven Network Inference
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2024-10-29 |
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nextclade
|
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
|
public |
The Galaxy object store framework and default implementations
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2024-10-29 |
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ucsc-bedgraphtobigwig
|
public |
Convert a bedGraph file to bigWig format.
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2024-10-29 |
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ucsc-wigtobigwig
|
public |
Convert ascii format wig file (in fixedStep, variableStep).
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2024-10-29 |
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kaptive
|
public |
Reports information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.
|
2024-10-28 |
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altamisa
|
public |
Alternative Python API for accessing ISA-tab files.
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2024-10-28 |
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libgff
|
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
|
public |
SEISMIC-RNA software by the Rouskin Lab
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2024-10-28 |
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dapcy
|
public |
An sklearn implementation of discriminant analysis of principal components (DAPC) for population genetics.
|
2024-10-28 |
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freyja
|
public |
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
|
2024-10-28 |
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merquryfk
|
public |
MerquryFK replaces meryl with the FastK k-mer counter suite to considerably speed up analyses.
|
2024-10-28 |
|
lima
|
public |
lima - The PacBio Barcode Demultiplexer
|
2024-10-28 |
|
fastk
|
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.
|
2024-10-28 |
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ucsc-pslcdnafilter
|
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.
|
2024-10-28 |
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pbaa
|
public |
PacBio tool to cluster HiFi reads and generate high quality consensus sequences
|
2024-10-28 |
|
pbstarphase
|
public |
A phase-aware pharmacogenomic diplotyper for PacBio sequencing data
|
2024-10-28 |
|
starfish
|
public |
Standardized analysis pipeline for image-based transcriptomics.
|
2024-10-28 |
|
hlafreq
|
public |
Download and combine HLA frequency data from multiple studies.
|
2024-10-28 |
|
sopa
|
public |
Spatial-omics pipeline and analysis.
|
2024-10-28 |
|
staden_io_lib
|
public |
Staden io_lib is a library of file reading and writing code e.g. for SAM/BAM/CRAM
|
2024-10-28 |
|
isoseq
|
public |
Iso-Seq - Scalable De Novo Isoform Discovery
|
2024-10-28 |
|
pbskera
|
public |
PacBio tool to split concatenated read designs
|
2024-10-28 |
|
masurca
|
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.
|
2024-10-28 |
|
shortstack
|
public |
ShortStack: Comprehensive annotation and quantification of small RNA genes
|
2024-10-28 |
|
kmer-jellyfish
|
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
|
2024-10-28 |
|
dajin2
|
public |
One-step genotyping tools for targeted long-read sequencing
|
2024-10-28 |
|
annembed
|
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
|
2024-10-28 |
|
nanoqc
|
public |
Create fastQC-like plots for Oxford Nanopore sequencing data.
|
2024-10-28 |
|
kinex
|
public |
Kinex infers causal kinases from phosphoproteomics data.
|
2024-10-28 |
|
d4binding
|
public |
The C/C++ binding for the D4 file format.
|
2024-10-28 |
|
maxit
|
public |
MAXIT assists in the processing and curation of macromolecular structure data.
|
2024-10-27 |
|
poseidon-trident
|
public |
A tool (trident) to work with modular genotype databases formatted using Poseidon.
|
2024-10-27 |
|
pretextgraph
|
public |
Embeds bedgraph data into Pretext contact maps.
|
2024-10-26 |
|
lofreq
|
public |
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
|
2024-10-26 |
|
haystac
|
public |
Species identification pipeline for both single species and metagenomic samples.
|
2024-10-26 |
|
strainy
|
public |
Assembly-based metagenomic strain phasing using long reads
|
2024-10-26 |
|
fastqe
|
public |
A emoji based bioinformatics command line tool.
|
2024-10-25 |
|
bindash
|
public |
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
|
2024-10-25 |
|
ucsc-blat
|
public |
Standalone BLAT v. 39x1 fast sequence search command line tool.
|
2024-10-25 |
|
flexiformatter
|
public |
Moving flexiplex barcode and UMI to bam tags
|
2024-10-25 |
|
pydeseq2
|
public |
A python implementation of DESeq2.
|
2024-10-25 |
