54 projects
sequana-pipetools
A set of tools to help building or using Sequana pipelines
sequana-pacbio-qc
QC on various type of pacbio data
sequana-quality-control
Quality control pipeline for NGS data (phix removal, adapter trimming, FastQC)
sequana-wrappers
Shell command library and Snakemake wrappers for Sequana pipelines
damona
A manager of singularity containers and their singularity recipes (NGS applications)
sequana-nanomerge
Merge barcoded or non barcoded fastq files generated by Nanopore runs
sequana
A set of standalone application and pipelines dedicated to NGS analysis
sequana-laa
Long read amplicon analysis
sequana-revcomp
reverse complement a set of FastQ files
sequana-downsampling
Downsample NGS data sets (FastQ/FastA) using the Sequana framework
sequana-slicer
SLicer detects splice leader sequences from long-read data using motif detection and soft-clip analysis.
sequana-multitax
A multi-sample and multi-databases taxonomic analysis using Kraken
sequana-ribofinder
A multi-sample identification of ribosomal content
sequana-variant-calling
A multi-sample variant calling pipeline
sequana-rnaseq
A RNAseq pipeline from raw reads to feature counts
idrix
IDR is a method for measuring the reproducibility of replicated ChIP-seq type experiments and providing a stable measure of the reproducibility of identified peaks.
sequana-chipseq
A ChIP-seq pipeline from raw reads to peaks
sequana-hic
Hi-C analysis, snakemake, sequana, container, reproducibility
sequana-denovo
Multi-sample denovo assembly of FastQ sequences (short read)
sequana-depletion
A pipeline to deplete reads from a given reference
sequana-bioconvert
description: convert NGS format from one to another using bioconvert
sequana-lora
Run assembler (Canu, Flye, Hifiasm) on a set of long read files
versionix
Get version of any tools
bioservices
Access to Biological Web Services from Python
sequana-demultiplex
Pipeline that runs bcl2fastq and ease demultiplexing of Sequencing data
sequana-multicov
Parallelised version of sequana_coverage standalone application
sequana-mapper
A multi-sample mapper to map reads onto a reference
bioconvert
convert between bioinformatics formats
fitter
A tool to fit data to many distributions and get the best one(s)
spectrum
Spectrum Analysis Tools
easydev
Common utilities to ease development of Python packages
sequanix
Sequanix is a graphical user interface (GUI) that can be used to run Snakemake workflows
colormap
Commn utilities to ease development of Python packages
sequana-fastqc
A multi-sample fastqc pipeline from Sequana project
mergegi
Merge MGI fastq files
biosniff
A sniffer for biological data formats
pysalsa
convert between bioinformatics formats
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
