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pysradb
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public |
Python package for interacting with SRAdb and downloading datasets from SRA
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2019-02-19 |
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igor_vdj
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public |
IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data.
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2019-02-18 |
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scnic
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public |
SCNIC: Sparse Cooccurence Network Investigation for Compositional data
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2019-02-18 |
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medaka
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public |
Neural network sequence error correction.
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2019-02-18 |
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fusioncatcher
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public |
Finder of Somatic Fusion Genes in RNA-seq data.
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2019-02-18 |
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digestiflow-cli
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public |
Command line client for Digestiflow.
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2019-02-18 |
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bioconda-utils
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public |
Utilities for building and managing bioconda recipes.
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2019-02-18 |
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deeptools
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public |
A set of user-friendly tools for normalization and visualzation of deep-sequencing data
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2019-02-18 |
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simple_sv_annotation
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public |
Simplify snpEff annotations for interesting cases
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2019-02-18 |
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anvio
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public |
An interactive analysis and visualization platform for omics data
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2019-02-18 |
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anvio-minimal
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public |
An interactive analysis and visualization platform for omics data
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2019-02-18 |
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scanpy-scripts
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public |
A set of wrappers for individual components of the scanpy package. Functions in python packages are hard to call when building workflows outside of python, so this package adds a set of simple wrappers with robust argument parsing.
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2019-02-18 |
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ensembl-vep
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public |
The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
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2019-02-18 |
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isocor
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public |
A Isotope Correction for mass spectrometry labeling experiments
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2019-02-18 |
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scanpy
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public |
Single-Cell Analysis in Python. Scales to >1M cells.
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2019-02-16 |
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anndata
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public |
An annotated data matrix.
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2019-02-16 |
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tango
|
public |
Assign taxonomy to metagenomic contigs using blastx searches
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2019-02-16 |
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mykrobe
|
public |
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.
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2019-02-16 |
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kaiju
|
public |
Fast and sensitive taxonomic classification for metagenomics
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2019-02-16 |
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whatshap
|
public |
phase genomic variants using DNA sequencing reads (haplotype assembly)
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2019-02-16 |
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sina
|
public |
Reference based multiple sequence alignment
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2019-02-16 |
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rapid
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public |
Read Alignment, Analysis, and Differential Pipeline (RAPID) is a set of tools for the alignment, and analysis of genomic regions with small RNA clusters derived from small RNA sequencing data.
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2019-02-16 |
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moff
|
public |
moFF is an OS independent tool designed to extract apex MS1 intensity using a set of identified MS2 peptides.
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2019-02-15 |
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fusioncatcher-seqtk
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public |
This is modified Seqtk version required for FusionCatcher.
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2019-02-15 |
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umis
|
public |
Tools for processing UMI RNA-tag data
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2019-02-15 |
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ataqv
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public |
ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.
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2019-02-15 |
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compare-reads
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public |
cythonized function to compare reads by name.
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2019-02-15 |
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jbrowse
|
public |
The JBrowse Genome Browser
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2019-02-15 |
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kipoi_veff
|
public |
kipoi_veff: variant effect prediction plugin for Kipoi
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2019-02-15 |
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shapeshifter
|
public |
A tool for managing and transforming large data sets
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2019-02-15 |
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snakemake
|
public |
Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files. This package provides the full installation including all optional dependencies.
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2019-02-15 |
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gromacs
|
public |
GROMACS is a versatile package to perform molecular dynamics.
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2019-02-15 |
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snakemake-minimal
|
public |
Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files. This package provides the core snakemake functionility. For features like reports and remote files, check out the snakemake package which provides all optional dependencies.
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2019-02-15 |
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maxbin2
|
public |
MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
|
2019-02-15 |
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infernal
|
public |
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.
|
2019-02-15 |
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wg-blimp
|
public |
wg-blimp (Whole Genome BisuLfIte sequencing Methylation analysis Pipeline) can be utilised to analyse WGBS data. It performs alignment, qc, methylation calling, DMR calling and DMR annotation using a multitude of tools.
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2019-02-15 |
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sniffles
|
public |
Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)
|
2019-02-15 |
|
pbccs
|
public |
pbccs - Generate Accurate Consensus Sequences from a Single SMRTbell
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2019-02-15 |
|
stream
|
public |
STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data http://stream.pinellolab.org
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2019-02-15 |
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staramr
|
public |
Scan genome contigs against the ResFinder and PointFinder databases
|
2019-02-15 |
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deeptoolsintervals
|
public |
A python module creating/accessing GTF-based interval trees with associated meta-data
|
2019-02-14 |
|
arb-bio-devel
|
public |
ARB 6 Sequence Analysis Suite
|
2019-02-14 |
|
arb-bio
|
public |
ARB 6 Sequence Analysis Suite
|
2019-02-14 |
|
arb-bio-tools
|
public |
ARB 6 Sequence Analysis Suite
|
2019-02-14 |
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libarbdb
|
public |
ARB 6 Sequence Analysis Suite
|
2019-02-14 |
|
fpa
|
public |
Filter Pairwise Alignment filter long read mapping information to save disk space
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2019-02-14 |
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socru
|
public |
Order and orientation of complete bacterial genomes
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2019-02-14 |
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r-basejump
|
public |
Base functions for bioinformatics and R package development.
|
2019-02-14 |
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seurat-scripts
|
public |
A set of wrappers for individual components of the Seurat 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 mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
|
2019-02-14 |
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ucsc-cell-browser
|
public |
A browser for single-cell data, main site at http://cells.ucsc.edu
|
2019-02-13 |