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mafft
|
public |
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
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2021-07-25 |
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aquilasv
|
public |
A region-based diploid assembly and variants calling tool
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2021-07-25 |
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lotus2
|
public |
LotuS2 is a lightweight complete 16S/18S/ITS pipeline
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2021-07-24 |
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sdm
|
public |
sdm - simple demultiplex tool for FASTQ demultiplexing and dereplication
|
2021-07-24 |
|
dadaist2
|
public |
Command line wrapper to run DADA2 on a set of paired-end reads
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2021-07-24 |
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deepsignal-plant
|
public |
A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads of plants
|
2021-07-24 |
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irida-staramr-results
|
public |
IRIDA StarAMR Results program enables StarAMR analysis results that were run through IRIDA to be batch downloaded into a collection of spreadsheets using the command line.
|
2021-07-24 |
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clair3-illumina
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public |
Clair3 with libraries to support variant calling using Illumina short-reads. Version in sync with Clair3.
|
2021-07-24 |
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aquila_sv
|
public |
Diploid assembly and variants calling tool
|
2021-07-24 |
|
phanotate
|
public |
Phanotate gene caller for phages
|
2021-07-24 |
|
isoquant
|
public |
IsoQuant is a tool for reference-based analysis of long RNA reads.
|
2021-07-24 |
|
pango-designation
|
public |
Repository for suggesting new lineages that should be added to the current
|
2021-07-24 |
|
aplanat
|
public |
Bokeh plotting API, with bio-focussed extras.
|
2021-07-24 |
|
tb-profiler
|
public |
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
|
2021-07-24 |
|
ultraplex
|
public |
fastq demultiplexer
|
2021-07-24 |
|
spades
|
public |
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
|
2021-07-23 |
|
serotypefinder
|
public |
SerotypeFinder identifies the serotype in total or partial sequenced isolates of E. coli.
|
2021-07-23 |
|
python-bioext
|
public |
A few handy bioinformatics tools not already in BioPython
|
2021-07-23 |
|
r-bcbiornaseq
|
public |
R package for bcbio RNA-seq analysis.
|
2021-07-23 |
|
cellprofiler
|
public |
CellProfiler is free, open-source software for quantitative analysis of biological images
|
2021-07-23 |
|
atlas-gene-annotation-manipulation
|
public |
Scripts for manipulating gene annotation
|
2021-07-23 |
|
ostir
|
public |
Open Source Transcription Initiation Rates
|
2021-07-23 |
|
kipoi-utils
|
public |
kipoi-utils: utils used in various packages related to kipoi
|
2021-07-23 |
|
treeswift
|
public |
TreeSwift: Fast tree module for Python 2 and 3
|
2021-07-23 |
|
dxpy
|
public |
DNAnexus Platform API bindings for Python
|
2021-07-23 |
|
ptools_bin
|
public |
Installation for ptools scripts.
|
2021-07-23 |
|
sscocaller
|
public |
Haplotyping single-cell DNA sequenced gamete cells.
|
2021-07-23 |
|
synapseclient
|
public |
Python client for Synapse
|
2021-07-23 |
|
r-signac
|
public |
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart and Butler et al. (2019) <doi:10.1016/j.cell.2019.05.031>.
|
2021-07-23 |
|
r-sigminer
|
public |
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
|
2021-07-23 |
|
arvados-python-client
|
public |
Python API for Arvados
|
2021-07-23 |
|
jcvi
|
public |
Python utility libraries on genome assembly, annotation and comparative genomics
|
2021-07-23 |
|
planemo
|
public |
Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
|
2021-07-23 |
|
trim-galore
|
public |
Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control
|
2021-07-23 |
|
salmon
|
public |
Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
|
2021-07-23 |
|
das_tool
|
public |
Recovery of genomes from metagenomes via a dereplication,
aggregation and scoring strategy.
|
2021-07-23 |
|
alevin-fry
|
public |
alevin-fry is a tool for the efficient processing of single-cell data based on RAD files produced by alevin
|
2021-07-22 |
|
deepbgc
|
public |
DeepBGC - Biosynthetic Gene Cluster detection and classification
|
2021-07-22 |
|
cellprofiler-core
|
public |
Dependency for CellProfiler v4
|
2021-07-22 |
|
r-acidplots
|
public |
Functions for plotting genomic data.
|
2021-07-22 |
|
trust4
|
public |
TCR and BCR assembly from bulk or single-cell RNA-seq data
|
2021-07-22 |
|
tasmanian-mismatch
|
public |
Tasmanian tool to analyze mismatches at read and position in high throughput sequencing data
|
2021-07-22 |
|
varlociraptor
|
public |
Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
|
2021-07-22 |
|
r-acidmarkdown
|
public |
Toolkit for extending the functionality of R Markdown.
|
2021-07-22 |
|
chewbbaca
|
public |
A complete suite for gene-by-gene schema creation and strain identification.
|
2021-07-22 |
|
scanpy-scripts
|
public |
Scripts for using scanpy from the command line
|
2021-07-22 |
|
miru-hero
|
public |
Compute MIRU and Spoligotype from a M. tuberculosis genome
|
2021-07-22 |
|
methyldackel
|
public |
A (mostly) universal methylation extractor for BS-seq experiments. Formerly named PileOMeth.
|
2021-07-22 |
|
scirpy
|
public |
A Scanpy extension for analyzing single-cell T-cell receptor sequencing data.
|
2021-07-22 |
|
dragonflye
|
public |
Microbial assembly pipeline for Nanopore reads
|
2021-07-22 |