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agfusion
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public |
Python package to annotate and visualize gene fusions.
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2024-09-30 |
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planemo
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public |
Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
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2024-09-24 |
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checkm-genome
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public |
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
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2024-09-23 |
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percolator
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public |
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
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2024-09-20 |
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fastq-screen
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public |
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
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2024-09-20 |
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fiji
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public |
Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
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2024-09-19 |
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repeatmasker
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public |
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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2024-09-17 |
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genomepy
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public |
Install and use genomes & gene annotations the easy way!
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2024-09-17 |
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vcflib
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public |
Command-line tools for manipulating VCF files.
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2024-09-17 |
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mirtop
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public |
Small RNA-seq annotation.
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2024-09-17 |
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cnv_facets
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public |
Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data
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2024-09-17 |
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pronto
|
public |
Python frontend to ontologies
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2024-09-15 |
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bioconvert
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public |
Convert between bioinformatics formats
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2024-09-13 |
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gdc-client
|
public |
GDC Data Transfer Tool
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2024-09-11 |
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synapseclient
|
public |
Python client for Synapse
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2024-09-10 |
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toulligqc
|
public |
A post sequencing QC tool for Oxford Nanopore sequencers.
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2024-09-10 |
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freebayes
|
public |
Bayesian haplotype-based polymorphism discovery and genotyping
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2024-09-10 |
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perl-mce-shared
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public |
MCE extension for sharing data supporting threads and processes
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2024-09-10 |
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graphmap
|
public |
A highly sensitive and accurate mapper for long, error-prone reads
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2024-09-09 |
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scnic
|
public |
SCNIC: Sparse Cooccurence Network Investigation for Compositional data
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2024-09-06 |
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clipandmerge
|
public |
Clip&Merge is a tool to clip off adapters from sequencing reads and merge overlapping paired end reads together.
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2024-09-05 |
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dedup
|
public |
DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
|
2024-09-05 |
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wisecondorx
|
public |
WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes
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2024-08-29 |
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perl-parallel-forkmanager
|
public |
A simple parallel processing fork manager
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2024-08-26 |
|
gxformat2
|
public |
Galaxy Workflow Format 2 Descriptions
|
2024-08-23 |
|
bpipe
|
public |
Bpipe - a tool for running and managing bioinformatics pipelines
|
2024-08-23 |
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pyseer
|
public |
Sequence Element Enrichment Analysis (SEER), python implementation
|
2024-08-22 |
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pipits
|
public |
PIPITS: An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform
|
2024-08-19 |
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treetime
|
public |
Maximum-Likelihood dating and ancestral inference for phylogenetic trees
|
2024-08-11 |
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pyani
|
public |
pyani provides a package and script for calculation of genome-scale average nucleotide identity.
|
2024-08-09 |
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nanoplot
|
public |
Plotting suite for long read sequencing data and alignments
|
2024-08-09 |
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cgpbigwig
|
public |
BigWig manpulation tools using libBigWig and htslib
|
2024-08-08 |
|
picrust2
|
public |
PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
|
2024-08-08 |
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sonicparanoid
|
public |
SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models
|
2024-08-07 |
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chewbbaca
|
public |
A complete suite for gene-by-gene schema creation and strain identification.
|
2024-08-06 |
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bam-readcount
|
public |
bam-readcount generates metrics at single nucleotide positions.
|
2024-08-05 |
|
r-ichorcna
|
public |
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
|
2024-08-01 |
|
perl-json
|
public |
JSON (JavaScript Object Notation) encoder/decoder
|
2024-07-31 |
|
morpheus
|
public |
mass spectrometry–based proteomics database search algorithm
|
2024-07-25 |
|
entrez-direct
|
public |
Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
|
2024-07-23 |
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pydna
|
public |
Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
|
2024-07-19 |
|
cancerit-allelecount
|
public |
Support code for NGS copy number algorithms
|
2024-07-17 |
|
graftm
|
public |
GraftM is a pipeline used for identifying and classifying marker gene reads from metagenomic datasets
|
2024-07-16 |
|
dropseq_tools
|
public |
Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab
|
2024-07-15 |
|
ucsc-cell-browser
|
public |
A browser for single-cell data, main site at http://cells.ucsc.edu. UCSC Cellbrowser, an interactive browser for single cell data. Includes importers and basic pipelines for text files, Seurat, Scanpy and Cellranger. All Javascript - does not require a server backend.
|
2024-07-09 |
|
bwakit
|
public |
A self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping
|
2024-07-02 |
|
rnaquast
|
public |
rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
|
2024-06-25 |
|
idr
|
public |
The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.
|
2024-06-25 |
|
tandem-genotypes
|
public |
Find tandem repeat length changes, from "long" DNA reads aligned to a genome
|
2024-06-25 |
|
concoct
|
public |
Clustering cONtigs with COverage and ComposiTion
|
2024-06-21 |
