RASflow: RNA-Seq Analysis Snakemake Workflow

RASflow is a modular, flexible and user-friendly RNA-Seq analysis workflow.

RASflow can be applied to both model and non-model organisms. It supports mapping RNA-Seq raw reads to both genome and transcriptome (can be downloaded from public database or can be homemade by users) and it can do both transcript- and gene-level Differential Expression Analysis (DEA) when transcriptome is used as mapping reference. It requires little programming skill for ...

Introduction

wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses ...

GRAVI: Gene Regulatory Analysis using Variable Inputs

This is a snakemake workflow for:

1. Performing sample QC
2. Calling ChIP peaks
3. Performing Differential Binding Analysis
4. Comparing results across ChIP targets

The minimum required input is one ChIP target with two conditions.

Full documentation can be found here

Snakemake Implementation

The basic workflow is written snakemake, requiring at least v7.7, and can be called using the following ...

ROIforMSI

Source codes for manuscript "Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation"

"ExampleWorkflow.ipynb" is a methods document to demonstrate the workflow of our multimodal fusion-based spatial segmentation.

"Utilities.py" contains all the tools to implement our method.

"gui.py" and "registration_gui.py" are files to implement linear and nonlinear registration.

(Licence: GPL-3)

We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a large dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.7244070. The dataset can be used as a reference for the identification of unknown samples. As unknown samples, we used data from Nawrocka et al. (2018), available at Zenodo: https://doi.org/10.5281/zenodo.7567336. Among others, the script can be used to identify the geographic ...

MoP2- DSL2 version of Master of Pores

[![Nextflow ...

sqtlseeker2-nf

A pipeline for splicing quantitative trait loci (sQTL) mapping.

The pipeline performs the following analysis steps:

• Index the genotype file
• Preprocess the transcript expression data
• Test for association between ...

mvgwas-nf

A pipeline for multi-trait genome-wide association studies (GWAS) using MANTA.

The pipeline performs the following analysis steps:

• Split genotype file
• Preprocess phenotype and covariate ...

Just the cleaning then assembly of all reads. TO explore further follow one of the paths described in "Global view" (WF 0)

Mapping against all plant virus then make contig out of the mapped reads then blast them.