AnnoAudit - Annotation Auditor

AnnoAudit is a robust Nextflow pipeline designed to evaluate the quality of genomic annotations through a multifaceted approach.

Overview of the workflow

The workflow assess the annotation quality based on different criteria:

• Protein evidence support
• RNASeq evidence support
• Statistics of the predictions (i.e., gene length, exon number, etc.)
• Ortholog analysis (BUSCO, OMArk)

Input data

• Reference genome genome.[.fna, .fa, .fasta]
• Annotation ...

Prostate cancer classification workflow

This workflow segments tissue regions and classifies prostate cancer on H&E whole slide images, using AI. It consists of three steps:

1. low-resolution tissue segmentation to select areas for further processing;

2. high-resolution tissue segmentation to refine borders - it uses step 1 as input;

3. high-resolution normal/cancer classification - it uses step 1 as input.

Tissue segmentation workflow

This workflow performs tissue segmentation on H&E whole slide images using AI.

PISAD - Phsaed Intraspecies Sample Anomalies Detection tool

Summary

We developed PISAD, a tool designed to detect anomalies in cohort samples without requiring reference information. It is primarily divided into two stages. Stage 1: We select low-error data from the cohort and conduct reference-free SNP calling to construct a variant sketch. Stage 2: By comparing the k-mer counts of other cohort data to the variant sketch, we infer the relationships between the sample and other samples to ...

REFLOW is a workflow manager tool designed to streamline and automate tasks related to renewable energy potential analyses. It is built with Luigi and provides an automated, robust framework for data acquisition, processing, land/sea eligibility analysis, technology placements, simulations and visualizations. It is build with transparency and reproducibility in mind.

FAIR Statistics Aggregator for DOIs

Table of Contents

1. Introduction
2. Features
3. Requirements
4. Installation
5. Usage
6. Output
7. Limitations
8. License

Introduction

This repository hosts a prototype tool designed to analyze and aggregate FAIR (Findable, Accessible, Interoperable, and Reusable) statistics for a list ...

RDM_system_connector

WARNING

This is a proof of concept, it has not been decided whether it will be developed into a fully functional tool. Feedback is therefore essential, especially as it is unclear whether this type of tool is useful at all, and if so, which parts, as the concept consists of many different parts. (source code readme:

• installation guide and short description
• [sphinx code ...

The workflow starts with selecting KLF4 as the search term. Gene sets with set labels containing KLF4 were queried from Enrichr[1]. Identified matching terms from the ENCODE TF ChIP-seq 2015[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ENCODE_TF_ChIP-seq_2015. Identified matching terms from the ChEA 2022[4] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ChEA_2022. Identified ...

The workflow starts with selecting Autophagy as the search term. Gene sets with set labels containing Autophagy were queried from Enrichr[1]. Identified matching terms from the MGI Mammalian Phenotype Level 4 2019[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for MGI_Mammalian_Phenotype_Level_4_2019. All the identified gene sets were combined using the union set operation. Reversers and mimickers from over 1 million signatures were identified ...

The workflow starts with selecting chr10:g.3823823G>A as the search term. The closest gene to the variant was found using MyVariant.info[1]. RNA-seq-like LINCS L1000 Signatures[3] which mimick or reverse the the expression of KLF6 were visualized. Median expression of KLF6 was obtained from the GTEx Portal[8] using the portal's API. To visualize the scored tissues, a vertical bar plot was created Fig..

1. Lelong, S. et al. BioThings SDK: a toolkit for building high-performance data APIs in ...