PARROT-FJD

Pipeline of Analysis and Research of Rare diseases Optimized in Tblab - Fundación Jiménez Díaz. This is a germline variant calling pipeline implemented in Nextflow which performs mapping, SNV/INDEL calling and annotation, and CNV calling and annotation for targeted sequencing (gene panels and WES) and whole genome sequencing.

How to run this pipeline

The different tasks previously mention are divided into different workflows which are specified usig the --analysis flag followed ...

NanoFreeLunch

Detecting DNA modifications quantitatively from Nanopore data without using raw signals.

Installation

1. Install Julia from https://julialang.org/. Do Not use Julia in containers like docker or singularity.
2. Enter the folder of NanoFreeLunch and type julia setup.jl.
3. The executable can be found in build/bin/, add the folder to PATH or add softlink of the executable to the folder in your PATH.

Warning: you might experience slow package downloading or get error like ...

[!NOTE] All data files in the src/ethos/tokenize/maps directory are under the CC0 public domain waiver.

ETHOS - EHR foundation model

This repository implements Adaptive Risk Estimation System (ARES) for Hospital Mortality, ICU Admission, Prolonged Length of Stay, and Composite (HM+IU+PLoS). In addition, it contains all the experiments conducted in our paper (preprint). It builds on our previous work on EHR foundation models by completely reimplementing ...

FREEPII (Feature Representation Enhancement End-to-end Protein Interaction Inference) is an end-to-end learning method encompassing autonomous feature extraction and feature representation enhancement for PPIs and protein complexes inference.

Portable genotype-free demultiplexing benchmarkign pipeline.

A portable pipeline for benchmarking genotype-free single-cell demultiplexing methods on simulated data.

The pipeline is designed to be generelisable to different datasets with arbitrary numbers of simulated mulitplexed samples. All software as part of pipeline is run through Apptainer containers to ensure reproducibility and ease of use. The pipeline default configuration is to be run on a cluster with a SLURM scheduler, but can be ...

demux_doublet_sim

Repository for Nextflow pipeline used in demuxSNP demultipelxing paper

Overall workflow

1. Simulate doublets

• Add per-sample suffix to barcodes in BAM
• Merge per-sample BAMs
• Generate lookup of barcodes to rename to reach a set % doublets
• Rename barcodes in BAM as per lookup

2. Benchmark methods

• Experiments 1: Vary doublet rate
• Experiment 2: Vary SNP subsetting

Inputs

Most inputs are specified in nextflow.config: container__souporcell: path to souporcell apptainer ...

PaSTa is a nextflow-based end-to-end image analysis pipeline for decoding image-based spatial transcriptomics data. It performs imaging cycle registration, cell segmentation and transcripts peak decoding. It is currently supports analysis of three types of ST technology:

• in-situ sequencing-like encoding
• MERFISH-like encoding
• RNAScope-like labelling

Prerequisites:

1. Nextflow. Installation guide: https://www.nextflow.io/docs/latest/getstarted.html
2. Docker or Singularity. Installation guide: ...

A workflow for performing alignment and phylogeny using protein sequences when studying genes/gene families.

RNA-SeqEZPZ-NF

Nextflow Pipeline for RNA-SeqEZPZ

A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations

RNA-SeqEZPZ-NF is another implementation of RNA-SeqEZPZ. RNA-SeqEZPZ-NF uses the same user interface as RNA-SeqEZPZ and runs the same pipeline, but runs the pipeline implemented by Nextflow. This pipeline is currently tested on HPC cluster with SLURM scheduler. Advanced ...

RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations

RNA-SeqEZPZ is a pipeline to run analysis of RNA-Seq experiments from raw FASTQ files all the way to differential genes analysis. The pipeline is accessible through a graphical user interface implemented using a Shiny app and features interactive plots. Advanced users have the ability to customize the scripts provided with the pipeline. This pipeline is designed to run on an HPC ...