Tools
RNAflow
A simple RNA-Seq differential gene expression pipeline using Nextflow.
The pipeline needs only Nextflow and Docker or Conda installed. For a test run, please try:
nextflow run hoelzer-lab/rnaflow -r v1.1.0 -profile test,local,docker
Please see the GitHub page for more detailed instructions and examples on how to use RNAflow.
RIBAP
Roary ILP Bacterial Annotation Pipeline
(This tool is currently under heavy development, so expect some bugs but feel free to report issues)
The pipeline needs only Nextflow and Docker or Conda installed:
nextflow run hoelzer-lab/ribap --fasta '*.fasta' --outdir ~/ribap_out
Please see the GitHub page for more detailed instructions and examples.
PoSeiDon
Positive Selection Detection and recombination analysis of protein-coding genes.
PoSeiDon now runs w/ Nextflow and Docker:
nextflow run hoelzer/poseidon --help
Please see the GitHub page for more detailed instructions and examples.
PCAGO
Interactive web service that allows analysis of RNA-Seq read count data with PCA and clustering.
- Go to web server
- Source code @GitHub
- Run PCAGO as standalone desktop application using the Electron framework
- Recommendation: run PCAGO locally using Docker (thx Lasse!)
We recommend to use Docker to run PCAGO on your local machine. If Docker is installed on your system, simply run:
docker run -p 8000:8000 --rm -it mhoelzer/pcago:1.0--c1e506c ./run_packrat.sh
Depending on your system permissions you might need to add --user $(id -u):$(id -g) as a parameter.
If you execute the Docker image on a server, simply connect to this server with port forwarding (not needed on your local machine):
ssh -L 8000:127.0.0.1:8000 your@your.server.com
In both cases you will then be able to access PCAGO via the following address in your browser: 127.0.0.1:8000.
SIM
SilentMutations (SIM) automatically constructs disrupting and restoring synonymous (silent) mutation pairs within coding regions for combinatorial in silico analysis of (viral) RNA-RNA interactions.
