raphael-group/paste_reproducibility

Paste reproducibility

Code to reproduce the analysis and figures in the paper Alignment and Integration of Spatial Transcriptomics Data. The Paste python package is located here. Note that this repo used Paste version 1.1.4 so any newer versions of Paste might have some issues (mostly likely related to minor utilities).

Datasets

• All preprocessed datasets can be found on zenodo.
• For convenience there is a script called download_data.sh that will download all the relevant files to the data directory in the correct hierarchy.

Main figures

• Figure 2
  • 2a
  • 2b
  • 2c
• Figure 3
• Figure 4
• Figure 5
• Figure 6

Extended Data figures

• ED Figure 1
• ED Figure 2
• ED Figure 3
• ED Figure 4
• ED Figure 5
• ED Figure 6
• ED Figure 7
• ED Figure 8
• ED Figure 9

Supplementary figures

• Figure S2
• Figure S3
• Figure S4
• Figure S5
• Figure S6
• Figure S7
• Figure S8
• Figure S9
• Figure S10
• Figure S11
• Figure S12
• Figure S13
• Figure S14
• Figure S15
• Figure S16
• Figure S17
• Figure S18
• Figure S19
• Figure S20
• Figure S21
• Figure S22
• Figure S23
• Figure S24
• Figure S25
• Figure S26
• Figure S27
• Figure S28
• Figure S29
• Figure S30