hammerlab immune-infiltrate-explorations issues

hammerlab / immune-infiltrate-explorations

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Hierarchical dispersion added to other-bucket model

#53 maximz opened 6 years ago
0
Decide how to package infino for release in user-friendly way

#52 maximz opened 7 years ago
0
"Other"/"Unknown" bucket model 6.4

#51 maximz closed 6 years ago
1
calculate percentiles of ground truth values in infino posterior distr's

#50 e5c closed 7 years ago
3
Ship informative priors (WIP)

#49 maximz closed 7 years ago
0
cibersort comparison master figure

#48 maximz closed 7 years ago
0
Update run_execute_ipynb.ml

#47 jburos opened 7 years ago
0
Adapting to new docker dev environment, reproducible gene lists, and Cibersort comparison figure

#46 maximz closed 7 years ago
0
Converted some old notebooks to python3

#45 maximz closed 7 years ago
0
Investigate RCC cohort that has bulk RNA-seq of TME and flow sorting data

#44 maximz opened 7 years ago
1
How to estimate uncertainty at each level of the immune cell type hierarchy?

#43 maximz closed 7 years ago
3
Out-of-sample synthetic mixtures tests and visual investigation of correlation matrix

#42 maximz closed 7 years ago
1
Remove data leakage in synthetic mixture tests

#41 maximz opened 7 years ago
0
Try variational inference models

#40 maximz opened 7 years ago
0
Plan how to model stromal and tumor cell content in mixtures

#39 maximz opened 7 years ago
0
Biokepi

#38 e5c closed 7 years ago
0
Abstract for Penn math/bio symposium

#37 e5c opened 7 years ago
0
Modify MSOS data.py to pull data from nfs-pool, not the g bucket

#36 e5c opened 7 years ago
0
Create setup.py, fix requirements.txt

#35 e5c opened 7 years ago
0
Remove kernelspec from ipynbs in `master` branch

#34 e5c opened 7 years ago
0
Review Dana Pe'er's model for scRNA seq using BISCUIT

#33 jburos opened 7 years ago
1
model5 negative parameter error

#32 e5c opened 7 years ago
7
strange pystan error when running model7

#31 jburos opened 7 years ago
0
Error message when running model7 with no cell-level features

#30 jburos opened 7 years ago
1
Model/stancache working properly?

#29 e5c closed 7 years ago
1
compare single-origin model inference to known tool output

#28 jburos opened 7 years ago
0
add adjustment for sample source (batch and/or project)

#27 jburos opened 7 years ago
0
execute all notebooks in single origin samples

#26 jburos opened 7 years ago
1
scale up fitting & testing of models (maybe using ketrew)

#25 jburos closed 7 years ago
1
simulate data according to our model

#24 jburos opened 7 years ago
3
Ketrewize Stan model training

#23 e5c opened 7 years ago
0
Schedule formal model review

#22 jburos opened 7 years ago
2
Document current mixture model

#21 jburos opened 7 years ago
0
Evaluate sequencing vendors for RNA isolated at MUSC and Sinai

#20 hammer opened 7 years ago
3
Generate data at ISMMS

#19 hammer opened 7 years ago
2
Name for this project/tool

#18 jburos opened 7 years ago
6
How to adjust for transcript length

#17 hammer opened 7 years ago
1
Try models using selected sets of genes

#16 hammer opened 7 years ago
2
Look into using alternate metrics

#15 hammer opened 7 years ago
2
Generate data at MUSC

#14 hammer opened 7 years ago
57
Update models

#13 jburos closed 8 years ago
0
Update models

#12 jburos closed 8 years ago
0
update 1.3 OOS performance nb

#11 jburos closed 8 years ago
0
add cell_type summary

#10 jburos closed 8 years ago
0
add more OOS model estimates

#9 jburos closed 8 years ago
0
Use stancache

#8 jburos closed 8 years ago
0
Out of sample prediction for single-cell types

#7 jburos opened 8 years ago
1
reorganized notebooks; updated model code; implemented caching

#6 jburos closed 8 years ago
0
Identify RNA-seq data for normal tissues

#5 jburos opened 8 years ago
3
Potential project with Ben Larman at JHU

#4 hammer opened 8 years ago
1