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Added new internal association test normalisr.association.association_test_5 that uses given mask to determine X-Y pairs in hypothesis tests with multi-variate regression. Refactored normalisr.association, normalisr.de, and normalisr.coex. Added option 'lowmem' to reduce memory footprint by not returning regression coefficients of covariates.
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| Metadata-Version: 2.1 | ||
| Name: normalisr | ||
| Version: 0.5.0 | ||
| Version: 0.6.0 | ||
| Summary: Normalisr Offers Robust Modelling of Associations Linearly In Single-cell RNA-seq | ||
| Home-page: https://github.com/lingfeiwang/normalisr | ||
| Author: Lingfei Wang | ||
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@@ -16,17 +16,17 @@ Description: ========= | |
| :target: https://zenodo.org/badge/latestdoi/242889849 | ||
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| Normalisr is a parameter-free normalization-association two-step inferential framework for scRNA-seq that solves case-control differential expression, co-expression, and pooled CRISPRi scRNA-seq screen under one umbrella of linear association testing. Normalisr addresses sparsity and technical confounding challenges of scRNA-seq with posterior mRNA abundances, nonlinear cellular summary covariates, and mean and variance normalization. All these enable linear association testing to achieve optimal sensitivity, specificity, and speed in all above scenarios. | ||
| Normalisr is a parameter-free normalization-association two-step inferential framework for scRNA-seq that solves case-control differential expression, co-expression, and pooled CRISPR scRNA-seq screen analysis with linear association testing. By systematically detecting and removing nonlinear confounding from library size, Normalisr achieves high sensitivity, specificity, speed, and generalizability across multiple scRNA-seq protocols and experimental conditions with unbiased P-value estimation. | ||
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| Normalisr follows the conventional framework of normalization/imputation of scRNA-seq, and aims to recover the true, biological, but hidden expression levels which any analyses may then operate upon. Then, linear association testing provides a unified inferential framework with numerous advantages: (i) exact P-value estimation without permutation, (ii) native removal of covariates as fixed effects, (iii) non-parametric robustness, (iv) unbeatable time and memory complexities, and (v) extension potentials such as variations in genetic relatedness. | ||
| Normalisr first removes confounding technical noises from raw read counts to recover the biological variations. Then, linear association testing provides a unified inferential framework with several advantages: (i) exact P-value estimation without permutation, (ii) native removal of covariates (*e.g.* batches, house-keeping programs, and untested gRNAs) as fixed effects, and (iii) computational efficiency. | ||
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| Normalisr is written in Python3 and provides a command-line and a python functional interface. You can read more about Normalisr from our preprint (See References_). | ||
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| Installation | ||
| ============= | ||
| Normalisr is on `PyPI <https://pypi.org/project/normalisr>`_ and can be installed with pip: ``pip install normalisr``. You can also install Normalisr from github: ``pip install git+https://github.com/lingfeiwang/normalisr.git``. Make sure you have added Normalisr's install path into PATH environment before using the command-line interface (See FAQ_). Normalisr's installation should take less than a minute. | ||
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| There are more advanced installation methods but if you want that, most likely you already know how to do it ;). If not, give me a shout (See Contact_). | ||
| There are more advanced installation methods but if you want that, most likely you already know how to do it. If not, give me a shout (See Contact_). | ||
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| Usage | ||
| ===== | ||
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@@ -60,26 +60,20 @@ Description: ========= | |
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| Contact | ||
| ========================== | ||
| We look forward to your feedbacks or questions of any kind. | ||
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| * Regarding method and manuscript, please reach me by email ([email protected]). | ||
| * Regarding Normalisr package, please raise an issue on `github <https://github.com/lingfeiwang/normalisr/issues/new>`_ or reach me by email ([email protected]). | ||
| Pease raise an issue on `github <https://github.com/lingfeiwang/normalisr/issues/new>`_ or reach me by e-mail ([email protected] or contact on the manuscript). | ||
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| References | ||
| ========================== | ||
| Please find the currently available materials below: | ||
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| * `Abstract <https://github.com/lingfeiwang/normalisr/raw/master/docs/preprint/ICML2020-WCB.pdf>`_ submitted to ICML 2020 Workshop on Computational Biology | ||
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| Contact_ me if you would like to request more details. | ||
| TBA | ||
|
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||
| FAQ | ||
| ========================== | ||
| * What does Normalisr stand for? | ||
| **N**\ ormalisr **O**\ ffers **R**\ obust **M**\ odelling of **A**\ ssociations **L**\ inearly **I**\ n **S**\ ingle-cell **R**\ NA-seq. Yes, it's a recursive acronym. See `GNU <https://www.gnu.org/gnu/gnu-history.en.html>`_ and `pip <http://www.ianbicking.org/blog/2008/10/28/pyinstall-is-dead-long-live-pip/index.html>`_. | ||
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| * I installed Normalisr but typing ``normalisr`` says 'command not found'. | ||
| \ | ||
| See below. | ||
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| * How do I use a specific python version for Normalisr's command-line interface? | ||
| You can always use the python command to run Normalisr, such as ``python3 -m normalisr`` to replace command ``normalisr``. You can also use a specific path or version for python, such as ``python3.7 -m normalisr`` or ``/usr/bin/python3.7 -m normalisr``. Make sure you have installed Normalisr for this python version. | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -8,17 +8,17 @@ Normalisr | |
| :target: https://zenodo.org/badge/latestdoi/242889849 | ||
|
|
||
|
|
||
| Normalisr is a parameter-free normalization-association two-step inferential framework for scRNA-seq that solves case-control differential expression, co-expression, and pooled CRISPRi scRNA-seq screen under one umbrella of linear association testing. Normalisr addresses sparsity and technical confounding challenges of scRNA-seq with posterior mRNA abundances, nonlinear cellular summary covariates, and mean and variance normalization. All these enable linear association testing to achieve optimal sensitivity, specificity, and speed in all above scenarios. | ||
| Normalisr is a parameter-free normalization-association two-step inferential framework for scRNA-seq that solves case-control differential expression, co-expression, and pooled CRISPR scRNA-seq screen analysis with linear association testing. By systematically detecting and removing nonlinear confounding from library size, Normalisr achieves high sensitivity, specificity, speed, and generalizability across multiple scRNA-seq protocols and experimental conditions with unbiased P-value estimation. | ||
|
|
||
| Normalisr follows the conventional framework of normalization/imputation of scRNA-seq, and aims to recover the true, biological, but hidden expression levels which any analyses may then operate upon. Then, linear association testing provides a unified inferential framework with numerous advantages: (i) exact P-value estimation without permutation, (ii) native removal of covariates as fixed effects, (iii) non-parametric robustness, (iv) unbeatable time and memory complexities, and (v) extension potentials such as variations in genetic relatedness. | ||
| Normalisr first removes confounding technical noises from raw read counts to recover the biological variations. Then, linear association testing provides a unified inferential framework with several advantages: (i) exact P-value estimation without permutation, (ii) native removal of covariates (*e.g.* batches, house-keeping programs, and untested gRNAs) as fixed effects, and (iii) computational efficiency. | ||
|
|
||
| Normalisr is written in Python3 and provides a command-line and a python functional interface. You can read more about Normalisr from our preprint (See References_). | ||
|
|
||
| Installation | ||
| ============= | ||
| Normalisr is on `PyPI <https://pypi.org/project/normalisr>`_ and can be installed with pip: ``pip install normalisr``. You can also install Normalisr from github: ``pip install git+https://github.com/lingfeiwang/normalisr.git``. Make sure you have added Normalisr's install path into PATH environment before using the command-line interface (See FAQ_). Normalisr's installation should take less than a minute. | ||
|
|
||
| There are more advanced installation methods but if you want that, most likely you already know how to do it ;). If not, give me a shout (See Contact_). | ||
| There are more advanced installation methods but if you want that, most likely you already know how to do it. If not, give me a shout (See Contact_). | ||
|
|
||
| Usage | ||
| ===== | ||
|
|
@@ -52,26 +52,20 @@ You can find more details in the respective examples. | |
|
|
||
| Contact | ||
| ========================== | ||
| We look forward to your feedbacks or questions of any kind. | ||
|
|
||
| * Regarding method and manuscript, please reach me by email ([email protected]). | ||
| * Regarding Normalisr package, please raise an issue on `github <https://github.com/lingfeiwang/normalisr/issues/new>`_ or reach me by email ([email protected]). | ||
| Pease raise an issue on `github <https://github.com/lingfeiwang/normalisr/issues/new>`_ or reach me by e-mail ([email protected] or contact on the manuscript). | ||
|
|
||
| References | ||
| ========================== | ||
| Please find the currently available materials below: | ||
|
|
||
| * `Abstract <https://github.com/lingfeiwang/normalisr/raw/master/docs/preprint/ICML2020-WCB.pdf>`_ submitted to ICML 2020 Workshop on Computational Biology | ||
|
|
||
| Contact_ me if you would like to request more details. | ||
| TBA | ||
|
|
||
| FAQ | ||
| ========================== | ||
| * What does Normalisr stand for? | ||
| **N**\ ormalisr **O**\ ffers **R**\ obust **M**\ odelling of **A**\ ssociations **L**\ inearly **I**\ n **S**\ ingle-cell **R**\ NA-seq. Yes, it's a recursive acronym. See `GNU <https://www.gnu.org/gnu/gnu-history.en.html>`_ and `pip <http://www.ianbicking.org/blog/2008/10/28/pyinstall-is-dead-long-live-pip/index.html>`_. | ||
|
|
||
| * I installed Normalisr but typing ``normalisr`` says 'command not found'. | ||
| \ | ||
| See below. | ||
|
|
||
| * How do I use a specific python version for Normalisr's command-line interface? | ||
| You can always use the python command to run Normalisr, such as ``python3 -m normalisr`` to replace command ``normalisr``. You can also use a specific path or version for python, such as ``python3.7 -m normalisr`` or ``/usr/bin/python3.7 -m normalisr``. Make sure you have installed Normalisr for this python version. | ||
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