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.gitignore Add gitignore for Rmd folder Mar 8, 2018
Aorta_facs.Rmd Don't TSNEPlot with free_annotation since it is all NA Jun 5, 2018
Aorta_facs.html Make utilities folder Mar 9, 2018
Aorta_facs.nb.html change to html Feb 27, 2018
Bladder_droplet.Rmd removed unneeded free annotation terms Apr 19, 2018
Bladder_droplet.nb.html Bladder: Deleted ridgeplot, commented out findmarkers Mar 13, 2018
Bladder_facs.Rmd Remove comparison to previous annotation Apr 19, 2018
Bladder_facs.nb.html Fix luminal/basal annotation for bladder cells in free annotation Mar 24, 2018
Brain_Microglia_facs.nb.html Fix bad commit (5c5b6a2) Mar 6, 2018
Brain_Myeloid_facs.Rmd Fixed brain problems, trachea formatting Mar 14, 2018
Brain_Non-Myeloid_facs.Rmd "astrocyte of cerebral cortex" to "astrocyte" Apr 19, 2018
Colon_facs.nb.html Use Colon_facs.nb.html from remote Mar 9, 2018
Diaphragm_facs.Rmd Rename avg_diff --> avg_logFC Mar 9, 2018
Diaphragm_facs.nb.html Make utilities folder Mar 9, 2018
Fat_facs.Rmd removed unneeded free annotation terms Apr 19, 2018
Fat_facs.nb.html Fat_facs now through "Nick_fat" branch Feb 27, 2018
Heart_and_Aorta_droplet.Rmd erythrocyte --> "NA" Jun 2, 2018
Heart_droplet.nb.html heart_droplet Feb 24, 2018
Heart_facs.Rmd "cardiac neuron" --> NA since no Rbfox3 or other neuronal markers Jun 2, 2018
Heart_facs.nb.html Rename tissues Mar 10, 2018
Kidney_droplet.Rmd natural killer cell --> leukocyte Jun 2, 2018
Kidney_droplet.nb.html Make utilities folder Mar 9, 2018
Kidney_facs.Rmd natural killer cell --> leukocyte Jun 2, 2018
Kidney_facs.html Make utilities folder Mar 9, 2018
Kidney_facs.nb.html fixed merge conflicts Mar 3, 2018
Large_Intestine_facs.Rmd compare_previous_cell_ontology_class --> compare_previous_annotation Mar 13, 2018
Limb_Muscle_droplet.Rmd removed unneeded free annotation terms Apr 19, 2018
Limb_Muscle_facs.Rmd removed unneeded free annotation terms Apr 19, 2018
Limb_Muscle_facs.nb.html Remove extraneous writing of annotation csvs Mar 24, 2018
Liver_droplet.Rmd Change uninformative free_annotations to NA Jun 4, 2018
Liver_droplet.nb.html Update autogenerated files Apr 19, 2018
Liver_facs.Rmd Change uninformative free_annotations to NA Jun 4, 2018
Liver_facs.nb.html Josh/vignette (#158) Mar 19, 2018
Lung_droplet.Rmd Fix bad commit (5c5b6a2) Mar 6, 2018
Lung_droplet.html Make utilities folder Mar 9, 2018
Lung_droplet.nb.html Updated the "<method>" portion of file names to match "<method>_". Mar 5, 2018
Lung_facs.Rmd Add Rmds from tissue_supplement branch Mar 9, 2018
Lung_facs.html Make utilities folder Mar 9, 2018
Lung_facs.nb.html Make utilities folder Mar 9, 2018
Makefile Add vignette rendering to makefile Jun 5, 2018
Mammary_Gland_droplet.Rmd removed unneeded free annotation terms Apr 19, 2018
Mammary_Gland_facs.Rmd Stash subtiss clusters in tiss Apr 19, 2018
Mammary_droplet.nb.html Make utilities folder Mar 9, 2018
Mammary_facs.nb.html Rename tissues Mar 10, 2018
Marrow_droplet.Rmd Don't plot TSNE on free annotation since everythign is NA Apr 19, 2018
Marrow_droplet.nb.html add html output of notebook Mar 19, 2018
Marrow_facs.Rmd Fix typo May 24, 2018
Marrow_facs.nb.html Clean up annotation for Marrow May 22, 2018
Muscle_droplet.nb.html Make utilities folder Mar 9, 2018
Muscle_facs.nb.html Make utilities folder Mar 9, 2018
Organ_Annotation_Vignette.Rmd Replaced 'tissue' with 'organ' Jun 5, 2018
Pancreas_facs.Rmd Change uninformative free_annotations to NA Jun 4, 2018
Pancreas_facs.nb.html Add error if subset not shown Apr 19, 2018
Skin_facs.Rmd Change uninformative free_annotations to NA Jun 4, 2018
Skin_facs.nb.html Updated the "<method>" portion of file names to match "<method>_". Mar 5, 2018
Spleen_droplet.Rmd removed unneeded free annotation terms Apr 19, 2018
Spleen_droplet.nb.html Make utilities folder Mar 9, 2018
Spleen_facs.Rmd Use function to save subclusters Mar 24, 2018
Spleen_facs.nb.html Make utilities folder Mar 9, 2018
Template.Rmd Fix bad commit (5c5b6a2) Mar 6, 2018
Thymus_droplet.Rmd professional antigen presenting cells --> leukocyte Jun 4, 2018
Thymus_droplet.nb.html verified Thymus-droplet Feb 27, 2018
Thymus_facs.Rmd professional antigen presenting cells --> leukocyte Jun 4, 2018
Thymus_facs.nb.html verified Thymus-droplet Feb 27, 2018
Tongue_droplet.Rmd removed unneeded free annotation terms Apr 19, 2018
Tongue_droplet.nb.html add ontology checking and update annotation file name Feb 21, 2018
Tongue_facs.Rmd Update Tongue_facs.Rmd Mar 20, 2018
Tongue_facs.nb.html Reran using boilerplate loader Feb 21, 2018
Trachea_droplet.Rmd Save subsets in tiss for Trachea facs Apr 19, 2018
Trachea_droplet.nb.html Make utilities folder Mar 9, 2018
Trachea_facs.Rmd Remove strings from NA Mar 24, 2018
Trachea_facs.nb.html Use William's trachea Mar 5, 2018
batch_replace_rmd.py Add cluster ids to saving Mar 5, 2018
boilerplate.R Clean up annotation for Marrow May 22, 2018
cell_ontology_submissions.md professional antigen presenting cells --> leukocyte Jun 4, 2018
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