48 projects
damona
A manager of singularity containers and their singularity recipes (NGS applications)
sequana-pipetools
A set of tools to help building or using Sequana pipelines
sequana-rnaseq
A RNAseq pipeline from raw reads to feature counts
sequana
A set of standalone application and pipelines dedicated to NGS analysis
sequana-multitax
A multi-sample and multi-databases taxonomic analysis using Kraken
fitter
A tool to fit data to many distributions and get the best one(s)
easydev
Commn utilities to ease development of Python packages
colormap
Commn utilities to ease development of Python packages
sequana-fastqc
A multi-sample fastqc pipeline from Sequana project
sequana-mapper
A multi-sample mapper to map reads onto a reference
sequana-variant-calling
A multi-sample variant calling pipeline
versionix
Get version of any tools
sequana-demultiplex
Pipeline that runs bcl2fastq and ease demultiplexing of Sequencing data
sequana-revcomp
reverse complement a set of FastQ files
sequana-bioconvert
description: convert NGS format from one to another using bioconvert
sequana-depletion
A pipeline to deplete reads from a given reference
sequana-ribofinder
A multi-sample identification of ribosomal content
sequana-nanomerge
Merge barcoded or non barcoded fastq files generated by Nanopore runs
sequana-denovo
Multi-sample denovo assembly of FastQ sequences (short read)
bioconvert
convert between bioinformatics formats
sequana-pacbio-qc
QC on various type of pacbio data
sequana-laa
Long read amplicon analysis
sequana-multicov
Parallelise version of sequana_coverage standalone application.
sequanix
Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows
bioservices
Access to Biological Web Services from Python
mergegi
Merge MGI fastq files
biosniff
A sniffer for biological data formats
sequana-downsampling
downsample NGS data sets
pysalsa
convert between bioinformatics formats
spectrum
Spectrum Analysis Tools
sequana-quality-control
A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix), performs fastqc, adapter cleaning and trimming and checks for contaminants
sequana-sphinxext
A set of sphinx extension for Sequana pipelines, wrappers and rules
biokit
Set of tools related to Bioinformatics (e.g., visualisation)
reports
Quickly create HTML reports using a set of JINJA templates
sequana-merge-flowcells
Merge FastQ from different projects (flowcells) into single project
sequana-coverage
Parallelise version of sequana_coverage standalone application.
gdsctools
Set of tools and pipelines to analyse GDSC data (cancerrxgene.org)
dreamtools
Scoring functions for the DREAM / SAGE challenges
pypiview
Utility to visualise the number of downloads of package(s) available on Pypi website
cno
CNO (Cell Net Optimiser): Manipulate, Visualise and Optimise Biological Networks to Perturbation Data.
msdas
Put a short description here
cellnopt.core
Functions to manipulate networks and data related to signalling pathways.
browse
Open a web page in a browser, as simple as that...
cellnopt.data
data and model repository for http://www.cellnopt.org project
pymeigo
Python wrapper of MEIGOR, a R optimisation package (http://www.iim.csic.es/~gingproc/meigo.html).
cellnopt.admin
Administrative tools used to manage cellnopt software (python and R)
rtools
utilities to ease manipulation of R packages using rpy2.
cellnopt.wrapper
CellNOpt R packages wrapper and utilities