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Nanostring-Biostats
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InSituType
An R package for performing cell typing in SMI and other single cell data
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Iss102 multi sample workflow
#114
patrickjdanaher
closed
2 years ago
0
Can we save progress at intermediate steps in case there's a crash?
#113
patrickjdanaher
closed
2 years ago
1
Insitutype error during iteration 8 of phase 3
#112
mtgregory
closed
2 years ago
1
Iss109 warn about missing anchor types
#111
patrickjdanaher
closed
2 years ago
0
mergeCells should be able to remove clusters
#110
patrickjdanaher
closed
2 years ago
1
better warning for when some cells are missing
#109
patrickjdanaher
closed
2 years ago
1
drop rescaling
#108
patrickjdanaher
closed
2 years ago
0
Iss106 find anchors bugfix
#107
patrickjdanaher
closed
2 years ago
0
find_anchor_cells() fails on Hwang dataset
#106
mtgregory
closed
2 years ago
1
Temptable bug fix
#105
patrickjdanaher
closed
2 years ago
1
Iss99 anchor stats
#104
patrickjdanaher
closed
2 years ago
0
Error at the end of semisupervised fitting
#103
mtgregory
closed
2 years ago
2
workflow: stratification across tissues
#102
patrickjdanaher
closed
2 years ago
1
need good defaults for subsample sizes
#101
patrickjdanaher
closed
2 years ago
1
how to get init cluster assignments if n_clusts == 0
#100
patrickjdanaher
closed
2 years ago
2
extract cos and logliks from anchors
#99
patrickjdanaher
closed
2 years ago
1
Flag bad anchors
#98
patrickjdanaher
closed
2 years ago
0
workflow: stratify by immunofluorescence
#97
patrickjdanaher
closed
2 years ago
1
error when running showcase
#96
patrickjdanaher
closed
2 years ago
1
lock anchor profiles
#95
patrickjdanaher
closed
2 years ago
1
stop requiring that "neg" be a named vector
#94
patrickjdanaher
closed
2 years ago
1
1-iter version for supervised cell typing
#93
patrickjdanaher
closed
2 years ago
1
anchor cells should be internally consistent
#92
patrickjdanaher
closed
2 years ago
3
bug in makeClusterNames
#91
patrickjdanaher
closed
2 years ago
1
rename cell types which shift away from their anchors
#90
patrickjdanaher
closed
2 years ago
3
bug in chooseClusterNumber
#89
patrickjdanaher
closed
2 years ago
1
perhaps nbclust shouldn't rescale its profiles
#88
patrickjdanaher
closed
2 years ago
2
utils and plots to help select anchor cells
#87
patrickjdanaher
opened
2 years ago
0
make anchors and fixed_profiles arguments agree
#86
patrickjdanaher
closed
2 years ago
2
cell types with too few anchor cells should be discarded
#85
patrickjdanaher
closed
2 years ago
1
max_iters argument isn't working
#84
patrickjdanaher
closed
2 years ago
1
findAnchorCells speed improvements
#83
patrickjdanaher
closed
2 years ago
2
update and run vignette
#82
patrickjdanaher
closed
2 years ago
0
Vignette
#81
patrickjdanaher
closed
2 years ago
0
main into vignette
#80
patrickjdanaher
closed
2 years ago
0
EM not CEM, and remove Estep_size
#79
patrickjdanaher
closed
2 years ago
0
general cleanup
#78
patrickjdanaher
closed
2 years ago
0
Create separate function for supervised cell typing
#77
patrickjdanaher
closed
2 years ago
0
Infrastructure and docs
#76
patrickjdanaher
closed
2 years ago
0
Anchor cells
#75
patrickjdanaher
closed
2 years ago
0
chooseClusterNumber function should be cleaned up
#74
patrickjdanaher
closed
2 years ago
1
Accounting for cell frequencies in calculating the likelihood
#73
zhiiiyang
closed
2 years ago
0
nbclust threw a error when n_clusts = 0
#72
zhiiiyang
closed
2 years ago
1
cleaning up the anchor cells branch
#71
patrickjdanaher
closed
2 years ago
0
should supervised cell typing still try to account for platform effects?
#70
patrickjdanaher
closed
2 years ago
1
fix #68
#69
zhiiiyang
closed
2 years ago
0
Error associated with `n_clusts=1`
#68
zhiiiyang
closed
2 years ago
0
once platform effects are settled, save computation time by not recomputing logliks under fixed profiles
#67
patrickjdanaher
closed
2 years ago
1
Iss65
#66
zhiiiyang
closed
2 years ago
0
`s` is not found while running `insitutype`
#65
zhiiiyang
closed
2 years ago
0
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