Abolfazl (Abe)

Is it possible to download datasets only once and use your package with those local files?

Improvements in the context of knowledge graph resources

10

Suggesting a new data function: **Knowledge Graph Mastery**, https://github.com/mims-harvard/TDC/discussions/23#discussioncomment-7364648 __Changes:__ - Add `knowledge_graph` module - Introduce `KnowledgeGraph` python class - Include `build_KG` function to enable creating graph from scratch -...

Expand cancer cell line and patient related datasets, e.g. DepMap, CCLE, TCGA

5

**Describe the problem** To enable cancer research, I would like to suggest including functionalities to work with cancer cell line information in TDC. In DepMap, there are updates in newer...

two gene sets GSEA, DGSEA module

2

Also requested here https://github.com/MaayanLab/blitzgsea/issues/7 ___ > Is there any chance that you can implement DGSEA in python as part of your package? > https://academic.oup.com/bioinformatics/article/36/21/5247/5874441 > https://jamesjoly.github.io/DGSEA/about/ > https://github.com/JamesJoly/DGSEA (developed by...

cc @PhilippSpahn

minor fixes for KG scripts

4

- [x] fill scripts missed from PR #207 - [x] fix and minor improvements in the `KnowledgeGraph` and `PrimeKGDev` classes - [ ] write unit tests for `primekg` api

bug in loading scPerturb datasets

3

Hi @kexinhuang12345, as you know `ReplogleWeissman2022` study has three datasets. ___ Currently, as I understand `ReplogleWeissman2022_K562_gwps` data is not uploaded. However, I noticed a weird behavior when I tried to...

Is there any chance that you can implement DGSEA in python as part of your package? - https://academic.oup.com/bioinformatics/article/36/21/5247/5874441 - https://jamesjoly.github.io/DGSEA/about/ - https://github.com/JamesJoly/DGSEA (developed by @JamesJoly in R)