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run space ranger on round4 data #23

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abspangler13 opened this issue Sep 28, 2021 · 0 comments
Closed

run space ranger on round4 data #23

abspangler13 opened this issue Sep 28, 2021 · 0 comments

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@abspangler13
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3 "new" samples
6432_ant_2
8325_mid_2
2720_ant_2

2 resequences
2720post
8667ant

1 missing resequence (emailed Linda)
6423mid
@abspangler13 abspangler13 self-assigned this Sep 28, 2021
@abspangler13 abspangler13 mentioned this issue Sep 28, 2021
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lcolladotor added a commit that referenced this issue Jul 14, 2022
@lcolladotor @Nick-Eagles @abspangler13
Resolve #23
c04a5e6 
We mostly adapted the code from
https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/dlpfc_snRNAseq_annotation.R
and also used functions in spatialLIBD that didn't exist when that script was
made by Andrew.

We only computed the `enrichment` t-statistics (one cluster vs others) and not
the `anova` or `pairwise` ones. Note that the correlation with the layer
`enrichment` t-statistics improved when we kept the top 100 genes per layer (and
WM). The inhibitory neuron don't seem to have much spatial registration.

We should discuss these results with everyone else in the spatial meeting.

Co-authored-by: Nick Eagles <nick.eagles@libd.org>
Co-authored-by: Abby Spangler <aspangle@gmail.com>
lcolladotor added a commit that referenced this issue Jul 14, 2022
@lcolladotor
Add plots related to c04a5e6 and #23
fbaecdf
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