Install

pip install genomenotebook

How to use

Create a simple genome browser with a search bar. The sequence appears when zooming in.

import genomenotebook as gn

g=gn.GenomeBrowser(genome_path, gff_path, init_pos=10000)
g.show()

Tracks can be added to visualize your favorite genomics data. See Examples for more !!!!

Address of the bookmark: https://dbikard.github.io/genomenotebook/

This is the demo application of the Carrot² clustering engine. It uses Carrot²'s algorithms to organize search results into thematic folders.

User interfaces

• Web Search Clustering organizes search results from public search engines into clusters; offers treemap- and pie-chart visualizations of the clusters.
• Clustering Workbench clusters content from local files in JSON or Excel format, Solr or Elasticsearch; allows tuning of clustering parameters and exporting results as Excel or JSON.

Search engines

• Web: web search results provided by etools.ch. Extensive use may require special arrangements with the owner of the etools.ch service.
• PubMed: abstracts of medical papers from the PubMed database provided by NCBI.
• Local file: content read from a local file in Carrot2 XML, JSON, CSV or Excel format.
• Solr: queries an Apache Solr instance.
• Elasticsearch: queries an Elasticsearch instance.

Clustering algorithms

• Lingo: creates well-described flat clusters. Does not scale beyond a few thousand search results. Available as part of the open source Carrot² framework.
• STC: the classic search results clustering algorithm. Produces flat cluster with adequate description, very fast. Available as part of the open source Carrot² framework
• k-means: base line clustering algorithm, produces bag-of-words style cluster descriptions. Available as part of the open source Carrot² framework

Address of the bookmark: https://search.carrot2.org/#/search/web

Despite the degrees you’ve earned, the effort and passion you put in every day, the sacrifices you make – academia burdens you with tons of stressors. Financial, psychological, physical, and more.

We’re an unconventional team with backgrounds in various fields – both inside and outside of academia. And through our lens, it’s clear that academia deeply undervalues and underserves its very own community!

It’s time to reimagine research.

Address of the bookmark: https://researchrabbitapp.com/

Address of the bookmark: https://github.com/pachterlab/gget

In an upset plot, each row represents a category or set, and each column represents a data point. The length of the bar for each category indicates the number of data points that belong to that category. The plot also shows the intersections between categories, represented by overlapping bars.

Upset plots are useful for visualizing complex data with multiple categories and intersections, and can help identify patterns and relationships between categories. They are often used in fields such as bioinformatics, where they can be used to analyze gene expression data or to compare the results of different experimental conditions.

https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions

Address of the bookmark: https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions

• In a GitHub or GitLab repository
• Free to use
• Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

The bioinformatics chat is produced by Roman Cheplyaka and hosted by Roman and Jacob Schreiber.

Address of the bookmark: https://bioinformatics.chat/

Open source machine learning and data visualization.

Build data analysis workflows visually, with a large, diverse toolbox.

Address of the bookmark: https://orangedatamining.com/

Address of the bookmark: https://github.com/sc932/ALE

https://wlcb.oit.uci.edu/modules/index.html

Address of the bookmark: https://wlcb.oit.uci.edu/NG-Circos