https://github.com/baderlab/lineage_vis
simulated lineage history files
https://github.com/baderlab/lineage_vis
Last synced: 4 months ago
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simulated lineage history files
- Host: GitHub
- URL: https://github.com/baderlab/lineage_vis
- Owner: BaderLab
- License: mit
- Created: 2025-02-14T17:55:30.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-14T23:47:10.000Z (over 1 year ago)
- Last Synced: 2025-10-05T18:41:22.993Z (8 months ago)
- Size: 1.84 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Lineage_Vis
simulated lineage history files
headings:
timestep -> simualtion steps at which the information was captured
cellname -> each cell has a unique name, this is important for single cell analysis. We can also track lineage by the name "1-1" parental name -> 1-1-1 or 1-1-2 for offspring
cell_Cycle_Time -> cell cycle duration set for the timestep
genome_state -> decribes the on (1) or off (0) state of genes in the system. it is describe as a string. each copy (ploiy) is separated by underscore _
genelist -> usually the names of genes in the system
offspring1_transcriptome -> describes how the transcript counts were randomly distributed to the offspring
offspring2_transcriptome -> describes how the transcript counts were randomly distributed to the offspring
Parent_cell_Cycle_Time -> the current cell cycle time
Offspring1_cell_Cycle_Time -> the inherited cell cycle time (may change depending on the parameters)
Offspring2_cell_Cycle_Time -> -> the inherited cell cycle time (may change depending on the parameters)
cell_Cycle_Phase -> the phase at which the cell was captured: 1 is G1, 2 is S, 3 is G2 and 4 is M
time_elapsed -> if this number is the same as Parent_cell_Cycle_Time it means the cell divided, however in a an asynchronous system some cells will be in the middle of a cell cycle when the information was captured and this collumn will tell you how far in the cell cycle they are