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mkdocs.yml
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site_name: kallisto | bustools
site_description: Short and simple bioinformatics tutorials
site_author: A. Sina Booeshaghi
copyright: "Copyright © 2021 - 2021 Pachterlab"
repo_url: https://github.com/pachterlab/kallistobustools
repo_name: pachterlab/kallistobustools
edit_uri: tree/master/tutorials/docs/
theme:
name: material
palette:
scheme: default
primary: teal
accent: amber
features:
- search.suggest
- search.highlight
language: en
google_analytics: ["UA-142178789-1", "kallistobus.tools"]
markdown_extensions:
- toc:
permalink: true
- admonition
- codehilite
- extra
- pymdownx.highlight:
linenums: true
linenums_style: pymdownx.inline
- pymdownx.inlinehilite
- pymdownx.superfences
- pymdownx.betterem:
smart_enable: all
extra:
social:
- type: "github"
icon: fontawesome/brands/github
link: "https://github.com/pachterlab"
- type: "twitter"
icon: fontawesome/brands/twitter
link: "https://twitter.com/sinabooeshaghi"
extra_css:
- css/custom.css
nav:
- Home: index.md
- Applications: applications.md
- Using kb:
- Introduction: kb_usage/kb_usage.md
- Building a reference: kb_usage/kb_ref.md
- Quantifying a dataset: kb_usage/kb_count.md
- Tutorials:
## Introduction
- Introduction to single-cell RNA-seq:
- Python: tutorials/scRNA-seq_intro/python/scRNA-seq_intro.md
- Preprocessing & Quality Control:
- Python: tutorials/kb_quality_control/python/kb_intro_1_python.md
- R: tutorials/kb_quality_control/R/kb_intro_1_R.md
- Getting started with analysis:
- Python: tutorials/kb_getting_started/python/kb_intro_2_python.md
- R: tutorials/kb_getting_started/R/kb_intro_2_R.md
## Analysis
- Building & annotating an atlas:
- Python: tutorials/kb_building_atlas/python/kb_analysis_0_python.md
- R: tutorials/kb_building_atlas/R/kb_analysis_0_R.md
- Pseudotime analysis:
- R: tutorials/kb_pseudotime/R/slingshot/kb_slingshot.md
- Single-nuclei RNA-seq:
- Python: tutorials/kb_nucleus/python/kb_single_nucleus.md
- RNA Velocity:
- Python: tutorials/kb_velocity/python/kb_velocity.md
- Feature barcode & multimodal data:
- Python: tutorials/kb_kite/python/kb_kite.md
## Other
- Find & download data: tutorials/download_data/data_download.md
- Build custom index:
- Python: tutorials/kb_custom_index/python/kb_transcriptome_index.md
- Build RNA velocity index:
- Python: tutorials/kb_velocity_index/python/kb_velocity_index.md
- Aggregate multiple matrices:
- Python: tutorials/kb_aggregate/python/kb_aggregating_count_matrices.md
- Process multiple FASTQs:
- Python: tutorials/kb_multiple_fastqs/python/kb_multiple_files.md
- Processing multi-species data:
- Python: tutorials/kb_species_mixing/python/kb_species_mixing.md
- R: tutorials/kb_species_mixing/R/kb_mixed_species_10x_v2.md
- Pseudotime analysis (Monocle2):
- R: tutorials/kb_pseudotime/R/monocle2/kb_monocle2.md