added comparisons and robustness

theislab · Jun 27, 2018 · 34d26cf · 34d26cf
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diff --git a/comparisons/nestorowa16_monocle2/nestorowa16_monocle2.ipynb b/comparisons/nestorowa16_monocle2/nestorowa16_monocle2.ipynb
diff --git a/comparisons/paul15_monocle2/monocle2_alternative.ipynb b/comparisons/paul15_monocle2/monocle2_alternative.ipynb
diff --git a/comparisons/paul15_monocle2/monocle2_original.ipynb b/comparisons/paul15_monocle2/monocle2_original.ipynb
diff --git a/comparisons/simulated_data/_exports.ipynb b/comparisons/simulated_data/_exports.ipynb
diff --git a/comparisons/simulated_data/dpt.ipynb b/comparisons/simulated_data/dpt.ipynb
diff --git a/comparisons/simulated_data/eclair/README.md b/comparisons/simulated_data/eclair/README.md
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+# Comparison with ECLAIR [(Giecold *et al.*, Nucl. Acids Research, 2016)](https://doi.org/10.1093/nar/gkw452)
+
+## Contents
+
+* [*eclair_plots*](eclair_plots.ipynb) visualizes the results of running eclair
+* [*logfile_run_X_krumsiek11_scaled.txt*](logfile_run_X_krumsiek11_scaled.txt) shows the logging output and the parameters that allow to reproduce the results discussed [here](../)
+* [*X_krumsiek11_scaled.txt*](X_krumsiek11_scaled.txt) contains the scaled data matrix for the simple tree, [*X_krumsiek11.txt*](X_krumsiek11.txt) contains the equivalent unscaled matrix and [*X_krumsiek11_blobs.txt*](X_krumsiek11_blobs.txt) contains the data describing tree and clusters; all in tab-separated format as required by ECLAIR. These files have been generated in [*../../comparisons_exports*](../../comparisons_exports.ipynb), which also provides visualizations of the data.
+
+## Notes
+
+* See the discussion of the results [here](../).
+
+* We acknowledge help by G. Giecold and S. P. Garcia, who adviced to scale the data matrix and provided default parameters. Parst of the correspondence are archived here: https://github.com/GGiecold/ECLAIR/issues/3
+
+* The algorithm could not handle the unnormalized data matrices [*X_krumsiek11.txt*](X_krumsiek11.txt) and [*X_krumsiek11_blobs.txt*](X_krumsiek11_blobs.txt).
diff --git a/comparisons/simulated_data/eclair/logfile_run_X_krumsiek11_scaled.txt b/comparisons/simulated_data/eclair/logfile_run_X_krumsiek11_scaled.txt
diff --git a/comparisons/simulated_data/monocle2.ipynb b/comparisons/simulated_data/monocle2.ipynb
diff --git a/comparisons/simulated_data/stemID/README.md b/comparisons/simulated_data/stemID/README.md
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+# Comparison with stemID 2
+
+Reproduce the comparison with stemID 2, the successor of stemID [(Grün *et al.*, Cell. Stem Cell,
+  2016)](https://doi.org/10.1016/j.stem.2016.05.010), 
+by running [*RaceID3_StemID2_sample.R*](RaceID3_StemID2_sample.R).
+```
+time Rscript RaceID3_StemID2_sample.R
+```
+See [*logfile_X_krumsiek11_blobs_shifted.txt*](*logfile_X_krumsiek11_blobs_shifted.txt*) for the logging output that we produced.
+
+We acknowledge D. Grün for providing the code via Email; parameters were chosen
+by D. Grün so that stemID would produce sensible results. The code is an
+improved version of the original stemID, which is available from https://github.com/dgrun/StemID/.
+
+We note that we also tried running the code on the simpler data file *X_krumsiek11_shifted.csv* with the same parameters, but were not able to do so as this resulted in errors.