Merge pull request #5 from eweitz/segment-docs

Document principles and example, enable use in Jupyter
eweitz · Jan 15, 2020 · 0a5dd6e · 0a5dd6e
2 parents 2154ad0 + 2197633
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diff --git a/degenome/dge_to_ideogram.py b/degenome/dge_to_ideogram.py
@@ -1,4 +1,4 @@
-'''Convert differential gene expression (DGE) matrix into Ideogram annotations
+'''Convert differential gene expression (DGE) matrix into Ideogram JSON
 
 This pipeline converts a DGE matrix file containing gene expression summary
 statistics into an Ideogram.js annotations JSON file.  The resulting JSON file

diff --git a/docs/_build/.DS_Store b/docs/_build/.DS_Store
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/environment.pickle~Stashed changes b/docs/_build/doctrees/environment.pickle~Stashed changes
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/index.doctree~Stashed changes b/docs/_build/doctrees/index.doctree~Stashed changes
diff --git a/docs/_build/doctrees/reduce-gtf.doctree b/docs/_build/doctrees/reduce-gtf.doctree
diff --git a/docs/_build/doctrees/transform-dge-matrix.doctree b/docs/_build/doctrees/transform-dge-matrix.doctree
diff --git a/docs/_build/doctrees/tutorial.doctree b/docs/_build/doctrees/tutorial.doctree
diff --git a/...d/html/_images/explore_differential_expression_across_the_genome_2020-01-11.png b/...d/html/_images/explore_differential_expression_across_the_genome_2020-01-11.png
diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
@@ -28,4 +28,7 @@ https://eweitz.github.io/ideogram/differential-expression.
    :maxdepth: 2
    :hidden:
 
-   installation
+   installation
+   reduce-gtf
+   transform-dge-matrix
+   tutorial
diff --git a/docs/_build/html/_sources/index.rst.txt~Stashed changes b/docs/_build/html/_sources/index.rst.txt~Stashed changes
@@ -0,0 +1,34 @@
+DEGenome – Differential expression across the genome
+====================================================
+|Build| |Coverage|
+
+
+DEGenome transforms differential gene expression (DGE) data to Ideogram_ JSON.
+
+Written in Python, the DEGenome pipeline takes in genome annotations and DGE
+matrices, and outputs Ideogram.js JSON annotation files.
+
+You can then upload Ideogram JSON to the cloud, and explore it in an
+interactive genome visualization at
+https://eweitz.github.io/ideogram/differential-expression.
+
+.. _Ideogram: https://github.com/eweitz/ideogram
+
+.. |Build| image:: https://img.shields.io/circleci/build/github/eweitz/degenome.svg
+  :target: https://circleci.com/gh/eweitz/degenome
+
+.. |Coverage| image:: https://codecov.io/gh/eweitz/degenome/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/eweitz/degenome
+
+.. image:: images/explore_differential_expression_across_the_genome.png
+  :width: 690
+  :alt: Explore differential expression across the genome
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   installation
+   reduce-gtf
+   transform-dge-matrix
+   tutorial
diff --git a/docs/_build/html/_sources/reduce-gtf.rst.txt b/docs/_build/html/_sources/reduce-gtf.rst.txt
@@ -0,0 +1,17 @@
+Reduce GTF
+==========
+Each organism processed by DEGenome will need a reduced GTF, i.e. a "gen_pos.tsv" file.
+
+The `gtf_to_gen_pos.py` CLI module converts a GTF genome annotation file from
+GENCODE, Ensembl, or NCBI into a smaller, simpler, and more metadata-rich TSV
+gene position ("gen_pos") file.  The purpose is to speed up, simplify, and
+enrich downstream pipelines that require only data on genes, and not e.g.
+transcripts or exons.
+
+Example GTF files
+^^^^^^^^^^^^^^^^^
+* `Human (Homo sapiens), from GENCODE <ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.basic.annotation.gtf.gz>`_
+* `Mouse (Mus musculus), from GENCODE <ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.basic.annotation.gtf.gz>`_
+* `Thale cress (Arabidopsis thaliana), from Ensembl <ftp://ftp.ensemblgenomes.org/pub/release-45/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.45.gtf.gz>`_
+* `Worm (Caenorhabditis elegans), from Ensembl <ftp://ftp.ensemblgenomes.org/pub/release-45/metazoa/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.45.gtf.gz>`_
+* `Rat (Rattus norvegicus), from Ensembl <ftp://ftp.ensembl.org/pub/release-98/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.98.chr.gtf.gz>`_
diff --git a/docs/_build/html/_sources/transform-dge-matrix.rst.txt b/docs/_build/html/_sources/transform-dge-matrix.rst.txt
diff --git a/docs/_build/html/_sources/tutorial.rst.txt b/docs/_build/html/_sources/tutorial.rst.txt
@@ -0,0 +1,6 @@
+Tutorial
+========
+
+For a walk-through example of using DEGenome to convert a differential gene expression
+matrix to Ideogram JSON, see the `"DEGenome tutorial" Jupyter Notebook on 
+Terra <https://app.terra.bio/#workspaces/degenome/degenome/notebooks/launch/degenome-tutorial.ipynb>`_.