The ultimate-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by layer 0 and 1 workflows, this workflow aims to enhance the quality of both acquisition images and processing.

Quality control protocols

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Combination of methods

• CTF consensus
• New methods to compare ctf estimations
• CTF xmipp criteria (richer parameters i.e. ice detection)

Advantages: 

• Control of ...

The second-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by the layer 0 workflow, this workflow aims to enhance the quality of acquisition images using quality protocols.

Quality control protocols

• Movie max shift: automatic reject those movies whose frames move more than a given threshold. 

• Tilt analysis: quality score based in the Power Spectrum Density (astigmatism and ...

The simplest workflow among a collection of workflows intended to solve tasks up to CTF estimation.

Basic processing pipeline

• Import movies

• Movie alignment (recommended 2 GPUs)

• CTF estimation

Monitor acquisition

• Monitor summary protocol: 
• Monitor basic parameters (item counts, drift, resolution, astigmatism, defocus, etc.)
• Raise alarms (mail setting available)
• Provides information of the basic steps (html report)

PAIRED-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT THE MOST ADAPTED VADR MODEL for annotation (see vadr parameters).

SINGLE-END workflow. Align reads on fasta reference/assembly using bwa mem, get a consensus, variants, mutation explanations.

IMPORTANT:

• For "bcftools call" consensus step, the --ploidy file is in "Données partagées" (Shared Data) and must be imported in your history to use the worflow by providing this file (tells bcftools to consider haploid variant calling).
• SELECT the mot ADAPTED VADR MODEL for annotation (see vadr parameters).

This repository contains the python code to reproduce the experiments in Dłotko, Gurnari "Euler Characteristic Curves and Profiles: a stable shape invariant for big data problems"

This workflow represents the Default ML Pipeline for AutoML feature from MLme. Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ...

We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.8128010. The dataset can be used as a reference for the identification of local bees from southern Kazakhstan, which most probably belong to the subspecies Apis mellifera pomonella. It was compared with data from Nawrocka et al. (2018), available at Zenodo: ...

The Polygenic Score Catalog Calculator (pgsc_calc)

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This workflow is designed to analyze to a multi-omics data set that comprises genome-wide DNA methylation profiles, targeted metabolomics, and behavioral data of two cohorts that participated in the ACTION Biomarker Study (ACTION, Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies. (Boomsma 2015, Bartels 2018, Hagenbeek 2020, van Dongen 2021, Hagenbeek 2022). The ACTION-NTR cohort consists of twins that are either longitudinally concordant ...