consenrich 0.0.1b1__tar.gz

consenrich-0.0.1b1/MANIFEST.in

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+include *.md
+recursive-include consenrich/ *.py
+recursive-include consenrich/refdata/ hg38.sizes
+recursive-include consenrich/refdata/ hg38_sparse.bed
+recursive-include consenrich/refdata/ hg38_blacklist.bed
+recursive-include consenrich/refdata/ mm10.sizes
+recursive-include consenrich/refdata/ mm10_sparse.bed
+recursive-include consenrich/refdata/ mm10_blacklist.bed
+recursive-include consenrich/refdata/ mm39.sizes
+recursive-include consenrich/refdata/ mm39_sparse.bed
+recursive-include consenrich/refdata/ mm39_blacklist.bed
+recursive-include consenrich/refdata/ dm6.sizes
+recursive-include consenrich/refdata/ dm6_sparse.bed
+recursive-include consenrich/refdata/ dm6_blacklist.bed
+recursive-include docs/ figure_1aa.png
+recursive-include docs/ ChIP_POL2RA_Demo.png

consenrich-0.0.1b1/PKG-INFO

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+Metadata-Version: 2.1
+Name: consenrich
+Version: 0.0.1b1
+Summary: Genome-wide extraction of reproducible continuous-valued signals hidden in noisy multisample functional genomics data
+Author: Nolan H. Hamilton, Benjamin D. McMichael, Michael I. Love, Terrence S. Furey
+Author-email: nolan.hamilton@unc.edu, bdmcmi@ad.unc.edu, milove@email.unc.edu, tsfurey@email.unc.edu
+License: MIT
+Keywords: genomics,functional genomics,epigenomics,epigenetics,signal processing,data fusion,state estimator,filter
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.11
+Requires-Dist: pandas
+Requires-Dist: pysam
+Requires-Dist: pybedtools
+Requires-Dist: deeptools
+Requires-Dist: pyBigWig
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+
+# Consenrich
+
+[![Tests](https://github.com/nolan-h-hamilton/Consenrich/actions/workflows/Tests.yml/badge.svg?event=workflow_dispatch)](https://github.com/nolan-h-hamilton/Consenrich/actions/workflows/Tests.yml)
+
+*Consenrich is a sequential genome-wide state estimator for extraction of reproducible, spatially-resolved, epigenomic signals hidden in noisy multisample HTS data.*
+
+---
+
+* **Input**:
+  * $m \geq 1$ Sequence alignment files `-t/--bam_files` corresponding to each sample in a given HTS experiment
+  * (*Optional*): $m_c = m$ control sample alignments, `-c/--control_files`, for each 'treatment' sample (e.g., ChIP-seq)
+
+* **Output**: Real-valued 'consensus' epigenomic state estimates (BedGraph/BigWig) and uncertainty metrics.
+  * As a robust, spatially informative representation of multiple samples' epigenomic profiles, Consenrich-extracted signal tracks can present additional insight for a variety of conventional analyses aiming to construct encompassing regulatory characterizations of sample groups (e.g., [consensus peak calling](docs/peaks_demo.png), mixed-assay peak calling, etc.)
+  * Consenrich also offers potential for various [spectral analyses](docs/filter_comparison.png), e.g., targeted detection of signal patterns associated with specific regulatory properties/states.
+
+Several technical features of Consenrich are discussed [below](#technical-features).
+
+## Example Command-Line Use
+
+* Run Consenrich on ten ATAC-seq samples in the current directory. Generate a BigWig signal track and inverse-variance-weighted residuals.
+
+   ```bash
+   consenrich --bam_files *.bam -g hg38 -o hg38_test_output.tsv --signal_bigwig demo_signal.bw --residual_bigwig demo_ivw_residuals.bw
+   ```
+
+![fig1](docs/figure_1aa.png)
+
+---
+
+* Use Consenrich for ChIP-seq enrichment analysis with treatment/control sample alignments (POL2RA, six donors' colon tissue samples). Generate separate BigWig output tracks for signal estimates and inverse-variance weighted residuals. Use fixed-width genomic intervals of 25bp:
+
+   ```bash
+  consenrich \
+    --bam_files \
+      ENCSR322JEO_POL2RA.bam \
+      ENCSR472VBD_POL2RA.bam \
+      ENCSR431EHE_POL2RA.bam \
+      ENCSR724FCJ_POL2RA.bam \
+      ENCSR974HQI_POL2RA.bam \
+      ENCSR132XRW_POL2RA.bam \
+    --control_files \
+      ENCSR322JEO_CTRL.bam \
+      ENCSR472VBD_CTRL.bam \
+      ENCSR431EHE_CTRL.bam \
+      ENCSR724FCJ_CTRL.bam \
+      ENCSR974HQI_CTRL.bam \
+      ENCSR132XRW_CTRL.bam \
+    -g hg38 --step 25 \
+    -o Consenrich_POL2RA.tsv \
+    --signal_bigwig Consenrich_POL2RA_CTRL_Signal.bw \
+    --residual_bigwig Consenrich_POL2RA_CTRL_IVW_Residuals.bw
+   ```
+
+**Output**
+![ChIPDemo](docs/ChIP_POL2RA_Demo.png)
+
+## Download/Install
+
+Consenrich can be easily downloaded and installed from source:
+
+1. `git clone https://github.com/nolan-h-hamilton/Consenrich.git`
+2. `cd Consenrich`
+3. `python setup.py sdist bdist_wheel`
+4. `python -m pip install .`
+5. Check installation: `consenrich --help`
+
+## Technical Features
+
+* Effectively models sample-and-region-varying noise to better integrate data across heterogeneous samples
+* Balances biologically-informed *a priori* predictions with observed HTS data to determine final estimates
+* Provides interpretable uncertainty quantification with respect to multiple model aspects
+* Runs efficiently in linear time with respect to genome size.

consenrich-0.0.1b1/README.md

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+# Consenrich
+
+[![Tests](https://github.com/nolan-h-hamilton/Consenrich/actions/workflows/Tests.yml/badge.svg?event=workflow_dispatch)](https://github.com/nolan-h-hamilton/Consenrich/actions/workflows/Tests.yml)
+
+*Consenrich is a sequential genome-wide state estimator for extraction of reproducible, spatially-resolved, epigenomic signals hidden in noisy multisample HTS data.*
+
+---
+
+* **Input**:
+  * $m \geq 1$ Sequence alignment files `-t/--bam_files` corresponding to each sample in a given HTS experiment
+  * (*Optional*): $m_c = m$ control sample alignments, `-c/--control_files`, for each 'treatment' sample (e.g., ChIP-seq)
+
+* **Output**: Real-valued 'consensus' epigenomic state estimates (BedGraph/BigWig) and uncertainty metrics.
+  * As a robust, spatially informative representation of multiple samples' epigenomic profiles, Consenrich-extracted signal tracks can present additional insight for a variety of conventional analyses aiming to construct encompassing regulatory characterizations of sample groups (e.g., [consensus peak calling](docs/peaks_demo.png), mixed-assay peak calling, etc.)
+  * Consenrich also offers potential for various [spectral analyses](docs/filter_comparison.png), e.g., targeted detection of signal patterns associated with specific regulatory properties/states.
+
+Several technical features of Consenrich are discussed [below](#technical-features).
+
+## Example Command-Line Use
+
+* Run Consenrich on ten ATAC-seq samples in the current directory. Generate a BigWig signal track and inverse-variance-weighted residuals.
+
+   ```bash
+   consenrich --bam_files *.bam -g hg38 -o hg38_test_output.tsv --signal_bigwig demo_signal.bw --residual_bigwig demo_ivw_residuals.bw
+   ```
+
+![fig1](docs/figure_1aa.png)
+
+---
+
+* Use Consenrich for ChIP-seq enrichment analysis with treatment/control sample alignments (POL2RA, six donors' colon tissue samples). Generate separate BigWig output tracks for signal estimates and inverse-variance weighted residuals. Use fixed-width genomic intervals of 25bp:
+
+   ```bash
+  consenrich \
+    --bam_files \
+      ENCSR322JEO_POL2RA.bam \
+      ENCSR472VBD_POL2RA.bam \
+      ENCSR431EHE_POL2RA.bam \
+      ENCSR724FCJ_POL2RA.bam \
+      ENCSR974HQI_POL2RA.bam \
+      ENCSR132XRW_POL2RA.bam \
+    --control_files \
+      ENCSR322JEO_CTRL.bam \
+      ENCSR472VBD_CTRL.bam \
+      ENCSR431EHE_CTRL.bam \
+      ENCSR724FCJ_CTRL.bam \
+      ENCSR974HQI_CTRL.bam \
+      ENCSR132XRW_CTRL.bam \
+    -g hg38 --step 25 \
+    -o Consenrich_POL2RA.tsv \
+    --signal_bigwig Consenrich_POL2RA_CTRL_Signal.bw \
+    --residual_bigwig Consenrich_POL2RA_CTRL_IVW_Residuals.bw
+   ```
+
+**Output**
+![ChIPDemo](docs/ChIP_POL2RA_Demo.png)
+
+## Download/Install
+
+Consenrich can be easily downloaded and installed from source:
+
+1. `git clone https://github.com/nolan-h-hamilton/Consenrich.git`
+2. `cd Consenrich`
+3. `python setup.py sdist bdist_wheel`
+4. `python -m pip install .`
+5. Check installation: `consenrich --help`
+
+## Technical Features
+
+* Effectively models sample-and-region-varying noise to better integrate data across heterogeneous samples
+* Balances biologically-informed *a priori* predictions with observed HTS data to determine final estimates
+* Provides interpretable uncertainty quantification with respect to multiple model aspects
+* Runs efficiently in linear time with respect to genome size.

consenrich-0.0.1b1/consenrich/__init__.py

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+from .consenrich import *
+from .misc_util import *