https://github.com/broadinstitute/cellbender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Science Score: 36.0%

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Found 4 DOI reference(s) in README
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2 of 6 committers (33.3%) from academic institutions
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Low similarity (14.6%) to scientific vocabulary

Keywords from Contributors

bioinformatics scrna-seq transcriptomics human-cell-atlas scverse single-cell-genomics single-cell-rna-seq

Last synced: 10 months ago · JSON representation

Repository

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Basic Info

Host: GitHub
Owner: broadinstitute
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://cellbender.rtfd.io
Size: 29.3 MB

Statistics

Stars: 353
Watchers: 9
Forks: 70
Open Issues: 161
Releases: 6

Created over 7 years ago · Last pushed 11 months ago

Metadata Files

Readme License

README.rst

CellBender
==========

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.. |badge1| image:: https://img.shields.io/github/license/broadinstitute/CellBender?color=white
   :target: LICENSE
   :alt: License

.. |badge2| image:: https://readthedocs.org/projects/cellbender/badge/?version=latest
   :target: https://cellbender.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status

.. |badge3| image:: https://img.shields.io/pypi/v/CellBender.svg
   :target: https://pypi.org/project/CellBender
   :alt: PyPI

.. |badge4| image:: https://static.pepy.tech/personalized-badge/cellbender?period=total&units=international_system&left_color=grey&right_color=blue&left_text=pypi%20downloads
   :target: https://pepy.tech/project/CellBender
   :alt: Downloads

.. |badge5| image:: https://img.shields.io/github/stars/broadinstitute/CellBender?color=yellow&logoColor=yellow)
   :target: https://github.com/broadinstitute/CellBender/stargazers
   :alt: Stars

.. image:: docs/source/_static/design/logo_250_185.png
   :alt: CellBender Logo

CellBender is a software package for eliminating technical artifacts from
high-throughput single-cell RNA sequencing (scRNA-seq) data.

The current release contains the following modules. More modules will be added in the future:

* ``remove-background``:

  This module removes counts due to ambient RNA molecules and random barcode swapping from (raw)
  UMI-based scRNA-seq count matrices.  Also works for snRNA-seq and CITE-seq.

Please refer to `the documentation `_ for a quick start tutorial.

   WARNING:
   
   The release tagged v0.3.1 included a bug which caused output count matrices to be incorrect. `The bug 
   `_, 
   introduced in `#303 `_, compromised output denoised count matrices 
   (due to an integer overflow) and would often show up as negative entries in the output count matrices. The bug also existed on 
   the master branch until `#347 `_.

   For now, we recommend using either v0.3.0 or the master branch (after #347) until v0.3.2 is released, and then using v0.3.2.

   Outputs generated with v0.3.1 (or the master branch between #303 and #347) can be salvaged by making use of the 
   checkpoint file, which is not compromised. The following command will re-run the (inexpensive, CPU-only) 
   estimation of the output count matrix using the saved posterior in the checkpoint file. Note the use of the new 
   input argument ``--force-use-checkpoint`` which will allow use of a checkpoint file produced by a different CellBender version:

   .. code-block:: console

     (cellbender) $ cellbender remove-background \
           --input my_raw_count_matrix_file.h5 \
           --output my_cellbender_output_file.h5 \
           --checkpoint path/to/ckpt.tar.gz \
           --force-use-checkpoint

   where ``path/to/ckpt.tar.gz`` is the path to the checkpoint file generated by the original run. Ensure that you pair up the right 
   ``--input`` with the right ``--checkpoint``.

Installation and Usage
----------------------

CellBender can be installed via

.. code-block:: console

  $ pip install cellbender

(and we recommend installing in its own ``conda`` environment to prevent
conflicts with other software).

CellBender is run as a command-line tool, as in

.. code-block:: console

  (cellbender) $ cellbender remove-background \
        --cuda \
        --input my_raw_count_matrix_file.h5 \
        --output my_cellbender_output_file.h5

See `the usage documentation `_
for details.


Using The Official Docker Image
-------------------------------

A GPU-enabled docker image is available from the Google Container Registry (GCR) as:

``us.gcr.io/broad-dsde-methods/cellbender:latest``

Available image tags track release tags in GitHub, and include ``latest``,
``0.1.0``, ``0.2.0``, ``0.2.1``, ``0.2.2``, and ``0.3.0``.


WDL Users
---------

A workflow written in the
`workflow description language (WDL) `_
is available for CellBender remove-background.

For `Terra `_ users, a workflow called
``cellbender/remove-background`` is
`available from the Broad Methods repository
`_.

There is also a `version available on Dockstore
`_.


Advanced installation
---------------------

From source for development
~~~~~~~~~~~~~~~~~~~~~~~~~~~

Create a conda environment and activate it:

.. code-block:: console

  $ conda create -n cellbender python=3.7
  $ conda activate cellbender

Install the `pytables `_ module:

.. code-block:: console

  (cellbender) $ conda install -c anaconda pytables

Install `pytorch `_ via
`these instructions `_, for example:

.. code-block:: console

   (cellbender) $ pip install torch

and ensure that your installation is appropriate for your hardware (i.e. that
the relevant CUDA drivers get installed and that ``torch.cuda.is_available()``
returns ``True`` if you have a GPU available.

Clone this repository and install CellBender (in editable ``-e`` mode):

.. code-block:: console

   (cellbender) $ git clone https://github.com/broadinstitute/CellBender.git
   (cellbender) $ pip install -e CellBender


From a specific commit
~~~~~~~~~~~~~~~~~~~~~~

This can be achieved via

.. code-block:: console

   (cellbender) $ pip install --no-cache-dir -U git+https://github.com/broadinstitute/CellBender.git@

where ```` must be replaced by any reference to a particular git commit,
such as a tag, a branch name, or a commit sha.


Citing CellBender
-----------------

If you use CellBender in your research (and we hope you will), please consider
citing our paper in Nature Methods:

Stephen J Fleming, Mark D Chaffin, Alessandro Arduini, Amer-Denis Akkad,
Eric Banks, John C Marioni, Anthony A Phillipakis, Patrick T Ellinor,
and Mehrtash Babadi. Unsupervised removal of systematic background noise from
droplet-based single-cell experiments using CellBender.
`Nature Methods`, 2023. https://doi.org/10.1038/s41592-023-01943-7

See also `our preprint on bioRxiv `_.

Owner

Name: Broad Institute
Login: broadinstitute
Kind: organization
Location: Cambridge, MA

Website: http://www.broadinstitute.org/
Twitter: broadinstitute
Repositories: 1,083
Profile: https://github.com/broadinstitute

Broad Institute of MIT and Harvard

GitHub Events

Total

Issues event: 27
Watch event: 45
Issue comment event: 47
Push event: 2
Pull request event: 7
Fork event: 14
Create event: 1

Last Year

Issues event: 27
Watch event: 45
Issue comment event: 47
Push event: 2
Pull request event: 7
Fork event: 14
Create event: 1

Committers

Last synced: about 1 year ago

All Time

Total Commits: 55
Total Committers: 6
Avg Commits per committer: 9.167
Development Distribution Score (DDS): 0.309

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Stephen Fleming	s****g	38
Mehrtash Babadi	m**h@b**g	11
alecw	a****w	3
Prete	m**e@s**k	1
Nikolay Markov	n**v@i**m	1
Jacob Kimmel	j**l@g**m	1

Committer Domains (Top 20 + Academic)

sanger.ac.uk: 1 broadinstitute.org: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 266
Total pull requests: 51
Average time to close issues: 7 months
Average time to close pull requests: about 1 month
Total issue authors: 201
Total pull request authors: 18
Average comments per issue: 3.4
Average comments per pull request: 1.35
Merged pull requests: 35
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 33
Pull requests: 8
Average time to close issues: about 1 month
Average time to close pull requests: about 22 hours
Issue authors: 31
Pull request authors: 7
Average comments per issue: 0.55
Average comments per pull request: 0.25
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sjfleming (30)
unikill066 (4)
smk5g5 (3)
jessicaliu70 (3)
apredeus (3)
racng (3)
Tycooner (3)
areyoukidneyme (2)
plijnzaad (2)
IrinaVKuznetsova (2)
Rfriedmancolumbia (2)
wmacnair (2)
samuel-marsh (2)
hemantgujar (2)
hviolaphd (2)

Pull Request Authors

sjfleming (28)
alecw (6)
dogTK (3)
jamestwebber (2)
colobas (2)
GreenGilad (2)
edg1983 (2)
aawdeh (2)
jpintar (2)
kshakir (1)
niklasmueboe (1)
caelen00000 (1)
mxposed (1)
prete (1)
ahmed-said-jax (1)

Top Labels

Issue Labels

user question (44) enhancement (31) bug (21) refactoring (4) docs (4) automation (1) contributions welcome (1) installation (1)

Pull Request Labels

bug (7) enhancement (2) refactoring (1)

Packages

Total packages: 1
Total downloads:
- pypi 1,475 last-month
Total docker downloads: 70

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 4
Total maintainers: 1

pypi.org: cellbender

A software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data

Homepage: http://github.com/broadinstitute/CellBender
Documentation: http://cellbender.readthedocs.io
License: BSD (3-Clause)
Latest release: 0.3.0
published almost 3 years ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 1,475 Last month
Docker Downloads: 70

Rankings

Dependent packages count: 7.0%

Average: 18.7%

Dependent repos count: 30.5%

Maintainers (1)

sjfleming

Last synced: 10 months ago

Dependencies

docker/Dockerfile docker

nvcr.io/nvidia/cuda 9.2-base-ubuntu16.04 build

setup.py pypi

line.rstrip *

ecosyste.ms

Data

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Open Source Science

https://github.com/broadinstitute/cellbender

Science Score: 36.0%

Keywords from Contributors

Repository

Basic Info

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Metadata Files

README.rst

Owner

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pypi.org: cellbender

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