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KrishnaswamyLab / MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
GNU General Public License v2.0
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Available codes to repeat results in Cell paper #134

Closed MichaelPeibo closed 6 years ago

MichaelPeibo commented 6 years ago

Hi, MAGIC team

Are there codes available to reproduce similar analysis in Cell paper? I found a link which seems to be a tutorial, but it reports a 404 error.

scottgigante commented 6 years ago

Hi @MichaelPeibo ,

Where was that link? I'll make sure to fix it to point to the right place.

There are two tutorials shown here: https://github.com/KrishnaswamyLab/MAGIC#tutorials

The EMT tutorial covers initial analysis of the EMT data shown in the paper. @dvdijk might be able to mention whether the full analysis code is available.

MichaelPeibo commented 6 years ago

Link I mentioned before is in here https://github.com/dpeerlab/magic

Interactive command line A tutorial on MAGIC usage and results visualization for single cell RNA-seq data can be found in this notebook: http://nbviewer.jupyter.org/github/pkathail/magic/blob/develop/notebooks/Magic_single_cell_RNAseq.ipynb

dvdijk commented 6 years ago

hi @MichaelPeibo Please see our tutorials. Our https://github.com/KrishnaswamyLab/scprep package provides tools for EMD differential expression analysis. For archetypal analysis please look for the PCHA method. I used it in matlab but there should be several packages available in python. Good luck!

MichaelPeibo commented 6 years ago

Hi, @dvdijk

Great! I will check it out.

BTW, nice and MAGIC method!