More than a list of tool names: these pages show, starting from real research scenarios, how several tools are combined into a complete chain of steps.
A complete workflow for estimating forest tree height from LiDAR point clouds or multi-source remote sensing imagery using QGIS and Python.
From preparing site data to running the APSIM NG maize model, analysing how climate and management practices affect yield.
A standardised workflow from raw data to submission-quality figures, covering R/Python plotting and post-processing in Inkscape.
A complete workflow from collecting literature, managing PDFs and reading notes to drafting the paper and inserting references.
A GIS mapping workflow from organising spatial data and unifying projections to producing thematic maps and publication-ready layouts.
A workflow for preprocessing, building training samples, classifying and assessing accuracy for Sentinel, Landsat or drone imagery.
A workflow from raw tables through cleaning, descriptive statistics, significance testing and figure export, ready for a paper's results.
Turn scanned PDFs, old papers and archival materials into searchable, copyable and manageable literature files.
A workflow for segmenting, counting, measuring and analysing microscopy images, disease images, particle images and tissue sections.
A workflow from drone photos to orthophotos, point clouds, DEM/DSM and basic terrain or vegetation analysis.
Cleaning, analysing and visualising keyword co-occurrence, citation networks, species interaction networks and other complex relational data.
Use free LibreOffice Base and MySQL to build a simple daily report entry and query system for a small team of about 10–20 people. Suits small companies, research groups, labs and project teams replacing paper reports and scattered Excel files at low cost.
Build a personal research homepage with free or open-source tools to present your bio, research areas, publications, project descriptions and tool downloads. Suits researchers, PhD students, research group members and freelance research consultants who want a long-term, maintainable personal site.
Organise scanned PDFs, downloaded papers and old materials into a Zotero library, and use OCR and a tagging system to improve search, reading and writing efficiency.
Systematically check the manuscript text, references, figures, tables, supplementary materials and PDF files before formal submission to reduce formatting errors and rework.
For everyday research users: start from an Excel or LibreOffice table and work through data cleaning, statistical analysis, exporting results and preparing paper tables and figures.
Batch-organise papers, reports, scanned materials and project files: merge, split, compress, rename, OCR and archive PDFs.
Starting from tabular or experimental data: prepare features, train, tune, validate and interpret models — suited to predictive modelling in research.
For disease recognition, microscopy image recognition, object detection and visual classification: organise images, annotate, run QA and split training sets.
For FASTQ sequencing data: organise raw data, check quality, filter, prepare for alignment and summarise everything in a MultiQC report.
Starting from 16S amplicon sequencing data and a sample metadata table: quality control, feature table construction, diversity analysis, differential analysis and visualisation.
Organising, anonymising, coding, thematically analysing and summarising interview transcripts, open-ended survey responses, field notes and other texts.
Organise data, code, documentation and supplementary materials related to a paper and publish them on an open science platform to obtain a citable link or DOI.
Use free or open-source tools to set up file sharing, task assignment, progress tracking, meeting materials and output archiving for a small research group.
You are welcome to contribute a tool workflow you have worked out in your research through GitHub.
Contribute on GitHub