STAGATE : https://www.nature.com/articles/s41467-022-29439-6#Sec1:
^documentation: https://stagate.readthedocs.io/en/latest/index.html
^github: https://github.com/QIFEIDKN/STAGATE / https://github.com/zhanglabtools/STAGATE/tree/main
GraphST : https://www.nature.com/articles/s41467-023-36796-3
^documentation: https://deepst-tutorials.readthedocs.io/en/latest/Installation.html
^github: https://github.com/JinmiaoChenLab/GraphST
^dataset: https://zenodo.org/record/6925603#.YuM5WXZBwuU
GLUE : https://www.nature.com/articles/s41587-022-01284-4#Sec8
^documentation: https://scglue.readthedocs.io/en/latest/install.html
^github: https://github.com/gao-lab/GLUE
^dataset:
Matilda : https://academic.oup.com/nar/article/51/8/e45/7076464?login=false
^documentation: https://scglue.readthedocs.io/en/latest/install.html
^github: https://github.com/PYangLab/Matilda
^youtube: https://www.youtube.com/watch?v=qdLH4dmHdkQ&ab_channel=Bioconductor
^dataset:
TotalVI : https://www.nature.com/articles/s41592-020-01050-x
Clip : https://arxiv.org/abs/2103.00020
^website: https://openai.com/research/clip
^simpler_documentation: (Tensorflow)https://www.kaggle.com/code/moeinshariatnia/openai-clip-simple-implementation/notebook
(Pytorch)https://towardsdatascience.com/simple-implementation-of-openai-clip-model-a-tutorial-ace6ff01d9f2
^github: https://github.com/openai/CLIP
^youtube: https://youtu.be/T9XSU0pKX2E
Contrastive Learning on Graphs (GRACE) : http://proceedings.mlr.press/v119/hassani20a.html
^github: https://github.com/CRIPAC-DIG/GRACE
PRECAST : http://proceedings.mlr.press/v119/hassani20a.html
^documentation: https://feiyoung.github.io/PRECAST/articles/PRECAST.Simu.html
^github: (Main)https://github.com/feiyoung/PRECAST
(Analysis)https://github.com/feiyoung/PRECAST_Analysis
All omics overview : https://www.nature.com/articles/s41576-023-00586-w#Sec35
SingleCell practices book : https://www.sc-best-practices.org/introduction/prior_art.html
Other:
Sprod : https://www.nature.com/articles/s41592-022-01560-w
SpaTalk : https://www.nature.com/articles/s41467-022-32111-8
Multigrate : https://www.biorxiv.org/content/10.1101/2022.03.16.484643v1.full.pdf
Variational Graph Auto-encoders (VGAE) : https://arxiv.org/abs/1611.07308
https://www.nature.com/articles/s43588-022-00266-5
https://www.nature.com/articles/s41592-020-01050-x
ScanPy :
https://scanpy.readthedocs.io/en/stable/tutorials.html
https://scanpy-tutorials.readthedocs.io/en/multiomics/cite-seq/pbmc5k.html
Scvi : https://docs.scvi-tools.org/en/stable/tutorials/index.html
PyroAI ScanANVI : https://pyro.ai/examples/scanvi.html
Scanpy&scvi Tutorial : https://ccbskillssem.github.io/assets/scvi_notebook.html
Seurat : R
Single cell : https://www.youtube.com/playlist?list=PLfaSRwcfHcq3p7Xu7SMQoR-S-e3Tg_ew6
https://www.youtube.com/@omicslogic/videos
https://www.youtube.com/@SingleCellOmicsGermany
multi omic data integration using message passing: https://www.youtube.com/watch?v=sgGAl2ZAxiA&ab_channel=winsseminar
Spatial omics data analysis https://www.youtube.com/playlist?list=PLBsJUKzoJTHSfWrLhCPCN-_vVU-klEi6p
^ course for above https://uppsala.instructure.com/courses/58516
https://www.youtube.com/watch?v=O3QzXWPjc74&ab_channel=CompBioSkillsSeminarUCBerkeley
^ notebook for this vid https://yu-tong-wang.github.io/talk/sc_st_data_analysis_R.html
Variational Graph AutoEncoders:
^ VGAE : https://www.youtube.com/watch?v=qA6U4nIK62E
^ GVAE explaination and training code : https://www.youtube.com/watch?v=xoSU9aDSy4U&list=PLV8yxwGOxvvoNkzPfCx2i8an--Tkt7O8Z&index=13&ab_channel=DeepFindr
^ Adversarial Regularizer VGAE : https://www.youtube.com/watch?v=qA6U4nIK62E
To run rpy2 if not able to import it, run this code instead.
import os
os.environ["R_HOME"] = r"C:\Program Files\R\R-4.3.0"
os.environ["PATH"] = r"C:\Program Files\R\R-4.3.0\bin\x64" + ";" + os.environ["PATH"]
import rpy2
import rpy2.robjects as robjects
from rpy2.robjects import pandas2ri, packages
pandas2ri.activate()
stats = packages.importr('stats')