La fabrique des restes

Homola, Stéphanie

doi:10.7202/1052636ar

Cited by 2 publications

(1 citation statement)

References 21 publications

(5 reference statements)

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“…Every step of the imputation framework has been completed on SLURM-based cluster on computed nodes with 16 CPU and 128GB RAM. We used the borutaPy package for Boruta implementation [ 41 ]. scOpen (version 1.0.0) and SCALE (version 1.0.1) packages were obtained at github.com.…”

Section: Methodsmentioning

confidence: 99%

scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting

Akhtyamov,

Shaheen,

Raevskiy

et al. 2023

Briefings in Bioinformatics

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Single-cell ATAC-seq (scATAC-seq) is a recently developed approach that provides means to investigate open chromatin at single cell level, to assess epigenetic regulation and transcription factors binding landscapes. The sparsity of the scATAC-seq data calls for imputation. Similarly, preprocessing (filtering) may be required to reduce computational load due to the large number of open regions. However, optimal strategies for both imputation and preprocessing have not been yet evaluated together. We present SAPIEnS (scATAC-seq Preprocessing and Imputation Evaluation System), a benchmark for scATAC-seq imputation frameworks, a combination of state-of-the-art imputation methods with commonly used preprocessing techniques. We assess different types of scATAC-seq analysis, i.e. clustering, visualization and digital genomic footprinting, and attain optimal preprocessing-imputation strategies. We discuss the benefits of the imputation framework depending on the task and the number of the dataset features (peaks). We conclude that the preprocessing with the Boruta method is beneficial for the majority of tasks, while imputation is helpful mostly for small datasets. We also implement a SAPIEnS database with pre-computed transcription factor footprints based on imputed data with their activity scores in a specific cell type. SAPIEnS is published at: https://github.com/lab-medvedeva/SAPIEnS. SAPIEnS database is available at: https://sapiensdb.com

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Section: Methodsmentioning

confidence: 99%

scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting

Akhtyamov,

Shaheen,

Raevskiy

et al. 2023

Briefings in Bioinformatics

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Chinese Eight Signs Prediction

Homola

2021

Social Analysis

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How do ontological assumptions in divination shape the structure of the techniques and the way practitioners understand their capacity to know about human fate? In eight signs divination—a birthdate-based method used to predict the fate of an individual—human lives are said to be determined by Heaven, an infallible and impersonal force that regulates everything in the cosmos through the expansionary flow of correlative cosmology and qi transformations. Such ontological assumptions correspond to epistemological operations as can be seen in the concrete working of eight signs divination in Taiwan. Eight signs prediction relies on classificatory and reductive mathematical procedures—involving congruence and combinatorial calculations—to logically unfold a deterministic and cyclical cosmos.

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La fabrique des restes

Cited by 2 publications

References 21 publications

scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting

scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting

Chinese Eight Signs Prediction

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