scrna-tools/scrna-tools

Table of software for the analysis of single-cell RNA-seq data.

scRNA-tools

A database of software tools for the analysis of single-cell RNA-seq data. To make it into the database software must be available for download and public use somewhere (CRAN, Bioconductor, PyPI, Conda, GitHub, Bitbucket, a private website etc). To view the database head to https://www.scRNA-tools.org.

Purpose

This database is designed to be an overview of the currently available scRNA-seq analysis software, it is unlikely to be 100% complete or accurate but will be updated as new software becomes available.

Contributing

We welcome contributions from the scRNA-seq community! If you would like to contribute please follow the have a look at the wiki or fill in the submission form on our website (https://www.scrna-tools.org/submit). Please be aware that by contributing you are agreeing to abide by the code of conduct.

If you are interested in joining the scRNA-tools team please contact us.

Citation

If you find the scRNA-tools database useful for your work please cite our publication:

Zappia L, Phipson B, Oshlack A. "Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database", PLOS Computational Biology (2018), DOI: 10.1371/journal.pcbi.1006245

@ARTICLE{,
  title       = "Exploring the single-cell {RNA-seq} analysis landscape with
                 the {scRNA-tools} database",
  author      = "Zappia, Luke and Phipson, Belinda and Oshlack, Alicia",
  journal     = "PLoS Computational Biology",
  volume      =  14,
  number      =  6,
  pages       = "e1006245",
  month       =  jun,
  year        =  2018,
  language    = "en",
  doi         = "10.1371/journal.pcbi.1006245",
  url         = "https://doi.org/10.1371/journal.pcbi.1006245",
}

If you make use of our analysis of the first 1000 tools in the database please also cite:

Zappia L, Theis FJ. "Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape", Genome Biology (2021), DOI: 10.1186/s13059-021-02519-4

@ARTICLE{,
  title    = "Over 1000 tools reveal trends in the single-cell {RNA-seq}
              analysis landscape",
  author   = "Zappia, Luke and Theis, Fabian J",
  journal  = "Genome Biol.",
  volume   =  22,
  number   =  1,
  pages    = "301",
  month    =  oct,
  year     =  2021,
  language = "en"
  doi      = "10.1186/s13059-021-02519-4",
  url      = "https://doi.org/10.1186/s13059-021-02519-4"
}

scrna-tools's Issues

Anaconda shields

Add shields for Anaconda repos

New categories

This is a list of suggested new categories to add to the database. If you have any other suggestions please comment below. Keep in mind that it is a significant amount of work to recategorise the tools currently in the database so any new categories will need to be sufficiently common or different to justify the effort 😸.

• Time-series - Tools that work with time-series data
• Cancer - Tools that work with cancer data
• Interactions - Interactions between cell types (ligand-receptor pairs)
• Design - Design and planning of experiments
• Perturbations - Analysis of perturbations (eg. drugs)
• Infrastructure - Tools that provide infrastructure, objects, data structures etc.
• Multiomics - Tools that combine multiple modalities (currently this is covered by Integration but maybe worth splitting to make more specific?)
• Metabolism - Tools that perform metabolomic modelling or other analysis of metabolism
• Other - General category for tools that don't fit anywhere else (and might need a new category in the future)

Add a tools landscape visualisation

A UMAP/tSNE visualisation showing how tools are related to each other. Something similar to this https://twitter.com/cleidson_alves/status/1206693726304776193.

Things this would require:

• Work out how to make the visualisation
• Add the visualisation code to the app
• Incorporate the visualisation into the website

Add contribution guidelines

Sorting locale

Set locale to avoid differences in sorting strings.

See https://stackoverflow.com/questions/39171613/sort-produces-different-results-in-ubuntu-and-windows for details.

DPT has wrong PubDate

DPT has the wrong PubDate (2019-08-29), unless it's come from the future :)

Paper incorrectly identified as preprint

A paper for the SHARP tool with the DOI 10.1101/gr.254557.119 is being incorrectly classified as a preprint by the app. We need to:

• Find out why this is happening
• Fix this in the app
• Check if any other papers are effected

Standardise platforms

Think about using only one of R/Python, Python/R etc.

Twitter cards

Add Twitter card support

Mention single-cell

Mention single-cell RNA-seq in the text somewhere on the website

Layout issues

On the webpage when scrolling the layout breaks and text starts to overlap

Collecting the information about citations

Hi there,
Thanks for the great website ! It is a useful resource. I wonder if you could help me extract the number of citations per published tool ? I am struggling trying to do it by myself.
Many thanks!
Cheers,
Elise

Add benchmarking studies

It might be useful to have a list of benchmarking studies with links to the tools they contain. Links to benchmarks could also be added to the tool entries.

A list of benchmarking studies collected by Mark Robinson is available here https://docs.google.com/spreadsheets/d/1Gqn0eZ8oiNh8-9ovyh4D_ZsoWcKYoKTJ0C1AfrJrdRA/edit#gid=0.

Implementing this would require:

• Finding relevant benchmark studies
• Adding new tables to the database to hold this information
• Modifying the app to use this information
• Adding a new page to the website
• Modifying the tools pages of the website
• Keeping the benchmarks list up to date

Check that new repositories don't match exisiting repositories

When running the check command in the app "new" repositories can be incorrectly found if they are new to the local packages cached but have already been added to the database (by somebody else). The app should check that any new matches are not the same as what is currently in that tool entry before suggesting them as new repositories.

Submit link

Add link to submit updates via email/form

Add data single cell modalities as categories

Thanks for this great resource! Would it be possible to add the single cell modality as a category or tag to enable further filtering of tools? E.g. scRNAseq, snRNAseq, scATACseq/multiome, CITE-seq, scVDJ etc.

Add license badges

See https://gist.github.com/lukas-h/2a5d00690736b4c3a7ba for links

Add descriptions to categories

Request: Add date information to table export

It would be nice to have the date added and date updated fields added to the table export. This would allow people to normalize citation count by date added in order to get a more apples-to-apples comparison of tool popularity.

Also, I don't know if you have data on when the pre-prints/papers supporting each tool were published, but that would be nice to include in both the table and tool views if available.

Bug in platforms plot

Thank you so much for maintaining this tool @lazappi !

I am currently updating my single cell overview slides and noticed an issue in the platforms barplot as the percentages do not sum up to 100% (see below).

Hopefully it's a quick fix :-)

Best

Cata

Replace rawgit serving

See https://rawgit.com/

Add UMI and SpikeIn column

Great table, very useful! It will be more helpful to add columns to indicate whether UMI count and spike-in (like ERCC) is supported.

Values in platforms analysis plot sum up to more than 100%

Hi folks! Thank you for the awesome resource! I've just noticed a bug on the analysis page - the platform plot doesn't seem to be displaying the correct percent values. I've attached a plot I downloaded today from the site:

That'll tally up to 117.7%

Seurat is not there https://www.scrna-tools.org/tools.html#Seurat

which is best clustering tool you will suggest for single-cell methods from scRNA-tools, i am very new in this so please suggest some.

Thanks