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flextaxd
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public |
Script that allows the creation of custom kraken databases from various sources (NCBI, QIIME, CanSNPer)
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2023-06-16 |
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whatsgnu
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public |
WhatsGNU A Tool For Identifying Proteomic Novelty
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2023-06-16 |
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biowdl-input-converter
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public |
Converting various input formats into WDL structs for BioWDL pipelines.
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2023-06-16 |
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cigar
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public |
manipulate SAM cigar strings
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2023-06-16 |
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seacr
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public |
SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage). It requires R (https://www.r-project.org) and Bedtools (https://bedtools.readthedocs.io/en/latest/) to be available in your path, and it requires bedgraphs from paired-end sequencing as input, which can be generated from read pair BED files (i.e. BED coordinates reflecting the 5' and 3' termini of each read pair) using bedtools genomecov with the "-bg" flag, or alternatively from name-sorted paired-end BAM files as described in "Preparing input bedgraph files" below.
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2023-06-16 |
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mavis
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public |
A Structural Variant Post-Processing Package
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2023-06-16 |
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perl-data-lock
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public |
makes variables (im)?mutable
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2023-06-16 |
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primerclip
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public |
Swift Accel-Amplicon primer trimming tool for fast alignment-based primer trimming
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2023-06-16 |
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samstats
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public |
SAM file alignment statistics at the read level
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2023-06-16 |
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encyclopedia
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public |
EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis
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2023-06-16 |
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perl-http-tiny
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public |
A small, simple, correct HTTP/1.1 client
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2023-06-16 |
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vpolo
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public |
Support package for Alevin tools
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2023-06-16 |
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patholive
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public |
A real-time pathogen diagnostics tool for metagenomic Illumina sequencing data.
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2023-06-16 |
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tagore
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public |
A simple way to visualize features on human chromosome ideograms
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2023-06-16 |
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umap
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public |
Umap and Bismap: tools for genome and methylome mappability
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2023-06-16 |
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salmid
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public |
Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).
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2023-06-16 |
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python-eel
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public |
Tool for finding evolutionarily conserved mammalian enhancer elements.
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2023-06-16 |
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xpressplot
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public |
A toolkit for navigating and analyzing gene expression datasets.
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2023-06-16 |
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panpasco
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public |
Pipeline for pangenome mapping and pairwise SNP distance
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2023-06-16 |
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fings
|
public |
Filters for Next Generation Sequencing
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2023-06-16 |
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blksheep
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public |
A package for differential extreme values analysis
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2023-06-16 |
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traitar
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public |
traitar - The microbial trait analyzer
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2023-06-16 |
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kggseq
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public |
KGGSeq is a software platform constituted of Bioinformatics and statistical genetics functions making use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants/genes responsible for human diseases/traits.
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2023-06-16 |
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atlas-metadata-validator
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public |
A MAGE-TAB validator for Expression Atlas and Single Cell Expression Atlas
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2023-06-16 |
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sepp-refgg138
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public |
SATe-enabled phylogenetic placement
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2023-06-16 |
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rop
|
public |
The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.
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2023-06-16 |
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sepp-refsilva128
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public |
SATe-enabled phylogenetic placement
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2023-06-16 |
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svanalyzer
|
public |
SVanalyzer: tools for the analysis of structural variation in genomes
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2023-06-16 |
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ena-dl
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public |
A tool to download FASTQs associated with Study, Experiment, or Run accessions.
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2023-06-16 |
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calib
|
public |
Clustering without alignment using (locality sensitive hashing) LSH and MinHashing of barcoded reads
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2023-06-16 |
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jmztab-m
|
public |
This project is the reference reader, writer and validator implementation for mzTab for metabolomics 2.0+.
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2023-06-16 |
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emmtyper
|
public |
Streptococcus pyogenes in silico EMM typer
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2023-06-16 |
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monocle3-cli
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public |
A set of wrappers for individual components of the monocle3 package. Functions R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently monocle3 R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
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2023-06-16 |
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aquila
|
public |
Diploid personal genome assembly and comprehensive variant detection based on linked-reads
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2023-06-16 |
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jupyterngsplugin
|
public |
Jupyter notebook plugin Bioinformatics NGS data analysis
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2023-06-16 |
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extract_fasta_seq
|
public |
To extract specific fasta sequences from a fasta file.
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2023-06-16 |
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msaconverter
|
public |
To convert multiple alignment alignments (MSA) into different formats
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2023-06-16 |
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python-goenrichment
|
public |
GO enrichment analysis from a list of gene names using a precomputed database
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2023-06-16 |
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taxonomy_ranks
|
public |
To get taxonomy ranks information for taxid, species name, or higher ranks (e.g., genus, family) with ETE3 from NCBI Taxonomy database.
|
2023-06-16 |
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bold-identification
|
public |
A tool for taxonomic assignment for given sequences using the BOLD database (http://www.boldsystems.org/index.php)
|
2023-06-16 |
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extract-codon-alignment
|
public |
To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.
|
2023-06-16 |
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ega2
|
public |
EGA download client v2
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2023-06-16 |
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logomaker
|
public |
Package for making Sequence Logos
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2023-06-16 |
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aquila_umap
|
public |
This is a program to generate Umap for Aquila diploid assembly.
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2023-06-16 |
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motifraptor
|
public |
Motif-centric analysis on GWAS data
|
2023-06-16 |
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pynnotator
|
public |
A Python Annotation Framework for VCFs using multiple tools.
|
2023-06-16 |
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uvp
|
public |
A Unified Variant Pipeline to identify variants and assign lineage from MTBC sequence data.
|
2023-06-16 |
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kounta
|
public |
Generate multi-sample k-mer count matrix
|
2023-06-16 |
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aquila_stlfr
|
public |
Diploid assembly and variants calling for stLFR and hybrid assembler for both linked-reads.
|
2023-06-16 |
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vmatch
|
public |
The Vmatch large scale sequence analysis software
|
2023-06-16 |
