pod5_by_pore

A Snakemake workflow to take the POD5 files produced by an Oxford Nanopore sequencing run and re-batch them by pore (ie. by channel).

This is useful if you want to run duplex basecalling because you can meaningfully run "dorado duplex" on a single (or a subset of) the POD5 files.

Know issues

It is assumed all POD5 input files are from the same sequencing run, but this is not checked.

beacon-omop-worker-workflows

GBMatch_CNN

Work in progress... Predicting TS & risk from glioblastoma whole slide images

Reference

Upcoming paper: stay tuned...

Dependencies

python 3.7.7

randaugment by Khrystyna Faryna: https://github.com/tovaroe/pathology-he-auto-augment

tensorflow 2.1.0

scikit-survival 0.13.1

pandas 1.0.3

lifelines 0.25.0

Description

The pipeline implemented here predicts transcriptional subtypes and survival of glioblastoma patients based on H&E stained whole slide scans. Sample data is ...

A hecatomb is a great sacrifice or an extensive loss. Heactomb the software empowers an analyst to make data driven decisions to 'sacrifice' false-positive viral reads from metagenomes to enrich for true-positive viral reads. This process frequently results in a great loss of suspected viral sequences / contigs.

For information about installation, usage, tutorial etc please refer to the documentation: https://hecatomb.readthedocs.io/en/latest/

Quick start guide

Install Hecatomb from Bioconda ...

JAX NGS Operations Nextflow DSL2 Pipelines

This repository contains production bioinformatic analysis pipelines for a variety of bulk 'omics data analysis. Please see the Wiki documentation associated with this repository for all documentation and available analysis workflows.

Complete workflow for TANGO as reported in Lecomte et al (2024), "Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling", Metabolic Eng. 83:24-38 https://doi.org/10.1016/j.ymben.2024.02.014

1. Parameters for individual models are obtained by optimization
2. Individual dynamics and community dynamics are simulated
3. Figures for the manuscript are assembled from the results.

ProGFASTAGen

The ProGFASTAGen (Protein-Graph-FASTA-Generator or ProtGraph-FASTA-Generator) repository contains workflows to generate so-called precursor-specific-FASTAs (using the precursors from MGF-files) including feature-peptides, like VARIANTs or CONFLICTs if desired, or global-FASTAs (as described in ProtGraph). The single workflow scripts have been implemented with Nextflow-DSL-2 ...

The input to this workflow is a data matrix of gene expression that was collected from a pediatric patient tumor patient from the KidsFirst Common Fund program [1]. The RNA-seq samples are the columns of the matrix, and the rows are the raw expression gene count for all human coding genes (Table 1). This data matrix is fed into TargetRanger [2] to screen for targets which are highly expressed in the tumor but lowly expressed across most healthy human tissues based on gene expression data collected ...

The tool provides a calculation of the power spectrum of Stochastic Gravitational Wave Backgorund (SGWB) from a first-order cosmological phase transition based on the parameterisations of Roper Pol et al. (2023). The power spectrum includes two components: from the sound waves excited by collisions of bubbles of the new phase and from the turbulence that is induced by these collisions.

The cosmological epoch of the phase transition is described by the temperature, T_star and by the number(s) of ...

gene2phylo

gene2phylo is a snakemake pipeline for batch phylogenetic analysis of a given set of input genes.

Contents

• Setup
• Example data
• Input
• Output
• Running your own data
• Getting help
• Citations

Setup

The pipeline is written in Snakemake and uses conda to install the necessary tools.

It is strongly recommended to install conda using Mambaforge. See details here ...