ALGAEFUN with MARACAS
microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS
Welcome to
ALGAEFUN
with
MARACAS
a microalgae web based tool for the analysis of
RNA-seq
and
ChIP-seq
data and the
functional annotation
of the resulting gene sets and genomic loci.
ALGAEFUN
with
MARACAS
supports the analysis for a wide collection
of microalgae that includes
Chlamydomonas reinhardtii, Ostreococcus tauri, Phaeodactylum tricornutum
and
Nannochloropsis gaditana.
Please select from the navigation bar on the left the type of analysis you want to perform. You can also
see our
video tutorials
on how to analyse RNA-seq and
ChIP-seq data as well as on how to functionally annotate gene sets and genomic loci. Our
code is freely available at
Github.
Please cite our work if you find it useful in your research.
Below you can find the phylogenetic relationship between the different microalgae species supported in ALGAEFUN with MARACAS:
AlgaeFUN
allows researchers to perform
functional annotation
over gene sets.
Gene Ontology (GO) enrichment
analysis as well as
KEGG (Kyoto Encyclopedia
of Genes and Genomes) pathway enrichment
analysis are supported. The gene set of interest can be obtained, for example,
as the result of a differential expression analysis carried out using
MARACAS.
See our
video tutorial
for details or follow the next steps to perform your analysis:
- In the left panel choose your microalgae of interest, the type of enrichment analysis to perform and the p-value threshold.
- Insert your gene set in the text box or load it from a file using the Browse … button. An example can be loaded by clicking on the Example button. Click on Clear button to remove the loaded gene set.
- Users can choose between the default background gene provided by AlgaeFUN of a custom one that can be specified.
- Click on the Have Fun button to perform the specified functional enrichment analysis. The results will be shown in the different tabs below.
PharaohFUN
has been updated.
Click here to acess the new site.
AlgaeFUN
allows researchers to perform
annotation analysis
of genomic loci or regions.
These are typically generated from
ChIP-seq
studies
of the genome-wide distribution of
epigenetic marks or transcription factor binding sites.
Our tool
MARACAS
can be used to perform this type of analysis. The set of marked genes
can be obtained as well as the distribution of the genomic loci overlapping specific genes parts. Also, individual marked genes
and the average signal level around the TSS (Transcription Start Site) and TES (Transcription
End Site) over the complete set of marked genes can be visualized.
See our
video tutorial
for details or follow the next steps to perform your analysis:
- In the left panel choose your microalgae of interest, the gene promoter length and the gene parts that will be considered when determining the marked genes.
- Insert in the text box your set of genomic regions as a table consisting of three tab-separated columns representing the chromosome, the start and end position of the regions. An example can be loaded by clicking on the Example button. Click on Clear button to remove the loaded gene set. Alternatively, using the Browse... button, the genomic regions can be uploaded from a file in BED format as described previously containing as least three columns. This file can be obained using our tool MARACAS.
- Optionally, users can upload the genome wide signal level of a epigenetic mark or transcription factor binding in a BigWig file. This file can be obained using our tool MARACAS.
- Click on the Have Fun button to perform the specified analysis. The results will be shown in the different tabs below.
MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS)
is an automatic computational pipeline specifically designed for the analysis of
microalgae RNA-seq and ChIP-seq data
. MARACAS starts processing raw fastq files
and generates lists of differentially expressed genes for RNA-seq data and lists of genomic
loci in bed format for ChIP-seq data. BigWig files containing normalized mapping signal are
also generated. The analysis are performed according to user specified parameters. Reports
in html and pdf format are produced for easy exploration of the results.
Differential expressed gene lists and genomic loci lists can be further analyzed using this online tool AlgaeFUN for functional analysis.
MARACAS supports a wide range of microalge including:
Differential expressed gene lists and genomic loci lists can be further analyzed using this online tool AlgaeFUN for functional analysis.
MARACAS supports a wide range of microalge including:
- Ostreococcus tauri
- Micromonas pusilla CCMP1545
- Bathycoccus prasinos
- Coccomyxa subellipsoidea
- Chlamydomonas reinhardtii
- Volvox Carteri
- Dunaliella salina
- Haematococcus lacustris
- Chlomochloris zofingiensis
- Klebsormidium nitens
- Mesotaenium endlicherianum
- Spirogloea muscicola
- Phaeodactylum tricornutum
- Nannochloropsis gaditana
AlgaeFUN,
is entirely developed using
the R package
shiny.
The
source code is released under
GNU General Public License v3.0
and is hosted at
GitHub.
If you experience any problem using AlgaeFUN please create an
issue
in GitHub and we will address it.
MARACAS,
is developed using bash scripting and several
bioconductor R packages. The source code is released under
GNU General Public License v3.0
and is hosted at
GitHub.
If you experience any problem using AlgaeFUN please create an
issue
in GitHub and we will address it.
We are strongly committed to
open access software
and
open science.
Following our philosophy we have deposited our GitHub code
into
Zenodo
, a
general-purpose open-access repository developed under the
European OpenAIRE program.
Meanwhile we publish
our work in a journal if you find
AlgaeFUN with MARACAS
useful in your research we would be most grateful if you cite
our GitHub repository with a,
DOI
as follows:
Romero-Losada, A.B., Arvanitidou, C., de los Reyes, P.,
García-González, M., Romero-Campero, F.J. (2021) AlgaeFUN with MARACAS, microAlgae FUNctional
enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS v1.0, Zenodo, doi:10.5381/zenodo.4754516 doi:10.5381/zenodo.4752818
Above you can find a video tutorial on how to use the different tools implemented in AlgaeFUN with MARACAS.
To watch the tutorial for PharaohFUN please press here
