Segmentation and Reference Point Detection for Laser Capture Microdissection (LMD)

Project Summary

This repository contains the code for a Cellpose-SAM & pyLMD project dedicated to automating cell boundary and reference point detection in microscopic images used for Laser Capture Microdissection (LMD).

The primary function of this repository is to identify the boundaries of target cells and detect ...

NanoporeDB_workflow

1. Overview

This repository contains the integrated computational workflow for the large-scale mining, multimeric structure prediction, and quality filtering of protein nanopores. This pipeline enables the discovery of novel nanopore candidates from massive metagenomic and genomic databases. The structural models, pore geometry analysis, and ...

Automated image processing from movies to 2D classification. Includes quality and curator micrgographs protocols as Dose analysis, maxshift, tilt analysis, categorize micrographs, ctf consensus, also include particle curator as Remove duplicates and Deep micrograph cleaner. It also include a support branch to calculate the Box Size and train a model to pick the particles. The list of plugins required are: pwem, xmipp3, motioncorr, miffi, cistem, emfacilities, sphire, gautomatch, relion, repic

Identify glycan and polysaccharide compositions from mass spectrometry files. The workflow itself performs a conversion of raw files, GlyCombo search, and visualisation of results.

FPNuNet: A Frequency-Aware Prompt-Guided Network for Nuclear Segmentation and Classification in Immunohistochemistry Images

This is the official code repository for "FPNuNet: A Frequency-Aware Prompt-Guided Network for Nuclear Segmentation and Classification in Immunohistochemistry Images".

Introduction

Accurate nuclear segmentation and classification (NuSC) in immunohistochemistry (IHC)-stained images is essential for reliable biomarker quantification, yet ...

name: "CI" on: [push, pull_request]

jobs: build: strategy: fail-fast: false matrix: ruby: ["2.5", "2.6", "2.7", "3.0"]

runs-on: macos-latest steps:

Setup env

• uses: actions/checkout@v2
• uses: ruby/setup-ruby@v1 with: ruby-version: "${{ matrix.ruby }}"

Show env

• name: Show macOS version run: sw_vers
• name: Show env versions run: | ruby --version bundler --version echo $HOME

Prepare

• name: Install bundler 2.2.20 run: gem install bundler -v "~> 2.2.20"
• name: Install ruby dependencies ...

Soil-WAter Quality model (SWAQ)

There are three main types of files:

1. *_AppPatt.R Used for building country specific Gemup (GEnaralised Mapped Usage Patterns). Only for CZ there is also CZ_PPPusage.R used for cleaning PPP usage data.

2. *_swaq_farm.R Used for calculating PEC and RQ at field level. Only CZ script is completed for the moment but NL and DK should follow similar template.

3. *_swaq_bas.R Used for calculating PEC and RQ at river catchment level. All scripts are completed. Only ...

Workflow (hybrid) metagenomic assembly and binning

• Workflow Illumina Quality: https://workflowhub.eu/workflows/336
• Sequali (control)
• hostile contamination filter
• fastp (quality trimming)
• Workflow Longread Quality: https://workflowhub.eu/workflows/337
• NanoPlot (control)
• fastplong (quality trimming)
• hostile contamination filter
• Kraken2 taxonomic classification of FASTQ reads
• SPAdes/Flye (Assembly) ...

EXCON (v2.3.1)

A Nextflow pipeline for gene family EXpansion and CONtraction analysis across multiple species using CAFE5.

Given a set of genome assemblies and annotations, EXCON builds orthogroups with OrthoFinder, fits and compares multiple CAFE models to identify gene families evolving at significantly different rates, and automatically selects the best-fitting model for downstream analysis. Optionally, GO enrichment analysis can be run on expanded and contracted gene families, and ...

Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)