Skip to content

fixed a few URLs #16

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
evanbiederstedt wants to merge 1 commit into
base: master
Choose a base branch
from
Open

fixed a few URLs #16

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@

![PAGA for hematopoiesis.](http://www.falexwolf.de/img/paga_paul15.png "PAGA for hematopoiesis.")

PAGA is available within [Scanpy](https://scanpy.readthedocs.io/en/latest/examples.html#trajectory-inference) through: [`tl.paga`](https://scanpy.readthedocs.io/en/latest/api/scanpy.tl.paga.html) | [`pl.paga`](https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.paga.html) | [`pl.paga_path`](https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.paga_path.html) | [`pl.paga_compare`](https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.paga_compare.html).
PAGA is available within [Scanpy](https://scanpy.readthedocs.io/en/stable/tutorials.html#trajectory-inference) through: [`tl.paga`](https://scanpy.readthedocs.io/en/latest/api/scanpy.tl.paga.html) | [`pl.paga`](https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.paga.html) | [`pl.paga_path`](https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.paga_path.html) | [`pl.paga_compare`](https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.paga_compare.html).

Below you find links to all central example notebooks, which also allow reproducing all main figures of the paper. If you start working with PAGA, go through [*blood/paul15*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/blood/paul15/paul15.ipynb).
Below you find links to all central example notebooks, which also allow reproducing all main figures of the paper. If you start working with PAGA, go through [*blood/paul15*](https://scanpy-tutorials.readthedocs.io/en/latest/paga-paul15.html).

notebook | system | details | reference | figure
---------------| ---------------| ---------| ----------| ------
Expand All @@ -27,9 +27,9 @@ notebook | description | figure
[*robustness*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/robustness) | robustness and multi-resolution capacity | S4, S5
[*comparisons/simulated_data*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/comparisons/simulated_data) | comparisons for simulated data | S6, S7
[*comparisons/paul15_monocle2*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/comparisons/paul15_monocle2) | comparison Monocle 2 for Paul *et al.* (2015) | S8
[*comparisons/nestorowa16_monocle2*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/comparisons/nestorowa16_monocle2) | comparison Monocle 2 for Nestorowa *et al.* (2016) | S9
[*comparisons/nestorowa16_monocle2*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/comparisons/nestorowa16_monocle2/nestorowa16_monocle2.ipynb) | comparison Monocle 2 for Nestorowa *et al.* (2016) | S9
[*embedding_quality*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/embedding_quality/embedding_quality.ipynb) | quantifying embedding quality | S10
[*simulation*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/blood/simulated/simulated.ipynb) | simulating hematopoiesis | S11
[*1M_neurons*](https://github.com/theislab/scanpy_usage/blob/master/170522_visualizing_one_million_cells/logfile_1.3M.txt) | neurons, 1.3 million cells, 10x Genomics, [10x Genomics (2017)](https://support.10xgenomics.com/single-cell-gene-expression/datasets/1M_neurons) | S12
[*blood/paul15*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/blood/paul15/paul15.ipynb) | annotation of louvain clusters using PAGA | S13
[*blood/paul15*](https://scanpy-tutorials.readthedocs.io/en/latest/paga-paul15.html) | annotation of louvain clusters using PAGA | S13
[*deep_learning*](https://nbviewer.jupyter.org/github/theislab/paga/blob/master/deep_learning/deep_learning.ipynb) | cycling Jurkat cells, 30,000 single-cell images, [Eulenberg *et al.*, Nat. Commun. (2017)](https://doi.org/10.1038/s41467-017-00623-3) | S14