Skip to content

Commit

Permalink
Documentation updates for 0.10.1
Browse files Browse the repository at this point in the history
  • Loading branch information
cflerin committed May 19, 2020
1 parent 0ef0119 commit bd27edc
Show file tree
Hide file tree
Showing 2 changed files with 41 additions and 24 deletions.
20 changes: 17 additions & 3 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,14 @@ in no time. The latter is achieved via the dask_ framework for distributed compu
News
----

2020-05-17
^^^^^^^^^^

**0.10.1 release**

* CLI: file compression (optionally) enabled for intermediate files for the major steps: grn (adjacencies matrix), ctx (regulons), and aucell (auc matrix). Compression is used when the file name argument has a .gz ending.


2020-02-27
^^^^^^^^^^

Expand Down Expand Up @@ -47,10 +55,15 @@ All the functionality of the original R implementation is available and in addit
3. Regulons, i.e. the regulatory network that connects a TF with its target genes, with targets that are repressed are now also derived and used for cell enrichment analysis.


Website
-------
Additional resources
--------------------

For more information, please visit LCB_, or SCENIC_ (R version).
The CLI to pySCENIC has also been streamlined into a pipeline that can be run with a single command, using the Nextflow workflow manager.
There are two Nextflow implementations available:

For more information, please visit LCB_, SCENIC_ (R version), or SCENICprotocol_ (for a Nextflow implementation).
* `SCENICprotocol`_: A Nextflow DSL1 implementation of pySCENIC alongside a basic "best practices" expression analysis. Includes details on pySCENIC installation, usage, and downstream analysis, along with detailed tutorials.
* `VSNPipelines`_: A Nextflow DSL2 implementation of pySCENIC with a comprehensive and customizable pipeline for expression analysis. Includes additional pySCENIC features (multi-runs, integrated motif- and track-based regulon pruning, loom file generation).


Acknowledgments
Expand Down Expand Up @@ -82,6 +95,7 @@ References
.. _arboreto: https://arboreto.readthedocs.io
.. _LCB: https://aertslab.org
.. _`SCENICprotocol`: https://github.com/aertslab/SCENICprotocol
.. _`VSNPipelines`: https://github.com/vib-singlecell-nf/vsn-pipelines
.. _notebooks: https://github.com/aertslab/pySCENIC/tree/master/notebooks
.. _issue: https://github.com/aertslab/pySCENIC/issues/new
.. _PyPI: https://pypi.python.org/pypi/pyscenic
Expand Down
45 changes: 24 additions & 21 deletions docs/installation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -115,31 +115,31 @@ A mount point (or more than one) needs to be specified, which contains the input
.. code-block:: bash
docker run -it --rm \
-v /path/to/data:/scenicdata \
aertslab/pyscenic:[version] pyscenic grn \
-v /data:/data \
aertslab/pyscenic:0.10.0 pyscenic grn \
--num_workers 6 \
-o /scenicdata/expr_mat.adjacencies.tsv \
/scenicdata/expr_mat.tsv \
/scenicdata/allTFs_hg38.txt
-o /data/expr_mat.adjacencies.tsv \
/data/expr_mat.tsv \
/data/allTFs_hg38.txt
docker run -it --rm \
-v /path/to/data:/scenicdata \
aertslab/pyscenic:[version] pyscenic ctx \
/scenicdata/expr_mat.adjacencies.tsv \
/scenicdata/hg19-tss-centered-5kb-7species.mc9nr.feather \
/scenicdata/hg19-tss-centered-10kb-7species.mc9nr.feather \
--annotations_fname /scenicdata/motifs-v9-nr.hgnc-m0.001-o0.0.tbl \
--expression_mtx_fname /scenicdata/expr_mat.tsv \
-v /data:/data \
aertslab/pyscenic:0.10.0 pyscenic ctx \
/data/expr_mat.adjacencies.tsv \
/data/hg19-tss-centered-5kb-7species.mc9nr.feather \
/data/hg19-tss-centered-10kb-7species.mc9nr.feather \
--annotations_fname /data/motifs-v9-nr.hgnc-m0.001-o0.0.tbl \
--expression_mtx_fname /data/expr_mat.tsv \
--mode "dask_multiprocessing" \
--output /scenicdata/regulons.csv \
--output /data/regulons.csv \
--num_workers 6
docker run -it --rm \
-v /path/to/data:/scenicdata \
aertslab/pyscenic:[version] pyscenic aucell \
/scenicdata/expr_mat.tsv \
/scenicdata/regulons.csv \
-o /scenicdata/auc_mtx.csv \
-v /data:/data \
aertslab/pyscenic:0.10.0 pyscenic aucell \
/data/expr_mat.tsv \
/data/regulons.csv \
-o /data/auc_mtx.csv \
--num_workers 6
Singularity
Expand Down Expand Up @@ -169,7 +169,7 @@ The first step (GRN inference) is shown as an example:
Using the Docker or Singularity images with Jupyter notebook
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
As of version 0.9.7, the pySCENIC containers have the `ipykernel` package installed, and can also be used interactively in a notebook.
As of version 0.9.7, the pySCENIC containers have the ``ipykernel`` package installed, and can also be used interactively in a notebook.
This can be achieved using a kernel command similar to the following (for singularity).
Note that in this case, a bind needs to be specified.
Expand All @@ -181,12 +181,15 @@ Note that in this case, a bind needs to be specified.
Nextflow
--------
The CLI to pySCENIC has also been streamlined into a pipeline that can be run with a single command, using the Nextflow workflow manager.
For details on this usage, along with more detailed pySCENIC tutorials, see the `SCENICprotocol`_ repository.
There are two Nextflow implementations available:
* `SCENICprotocol`_: A Nextflow DSL1 implementation.
* `VSNPipelines`_: A Nextflow DSL2 implementation.
.. _`Singularity Hub`: https://www.singularity-hub.org/collections/2033
.. _`SCENICprotocol`: https://github.com/aertslab/SCENICprotocol
.. _`VSNPipelines`: https://github.com/vib-singlecell-nf/vsn-pipelines
.. _dask: https://dask.pydata.org/en/latest/
.. _distributed: https://distributed.readthedocs.io/en/latest/
.. _`Docker Hub`: https://hub.docker.com/r/aertslab/pyscenic
Expand Down

0 comments on commit bd27edc

Please sign in to comment.