hammerlab/immune-infiltrate-explorations issues and pull requests

#53 - Hierarchical dispersion added to other-bucket model

Pull Request - State: open - Opened by maximz almost 7 years ago

#53 - Hierarchical dispersion added to other-bucket model

Pull Request - State: open - Opened by maximz almost 7 years ago

#52 - Decide how to package infino for release in user-friendly way

Issue - State: open - Opened by maximz about 7 years ago

#52 - Decide how to package infino for release in user-friendly way

Issue - State: open - Opened by maximz about 7 years ago

#51 - "Other"/"Unknown" bucket model 6.4

Pull Request - State: closed - Opened by maximz about 7 years ago - 1 comment

#51 - "Other"/"Unknown" bucket model 6.4

Pull Request - State: closed - Opened by maximz about 7 years ago - 1 comment

#50 - calculate percentiles of ground truth values in infino posterior distr's

Pull Request - State: closed - Opened by e5c about 7 years ago - 3 comments

#50 - calculate percentiles of ground truth values in infino posterior distr's

Pull Request - State: closed - Opened by e5c about 7 years ago - 3 comments

#49 - Ship informative priors (WIP)

Pull Request - State: closed - Opened by maximz about 7 years ago

#49 - Ship informative priors (WIP)

Pull Request - State: closed - Opened by maximz about 7 years ago

#48 - cibersort comparison master figure

Pull Request - State: closed - Opened by maximz about 7 years ago

#47 - Update run_execute_ipynb.ml

Pull Request - State: open - Opened by jburos about 7 years ago

#47 - Update run_execute_ipynb.ml

Pull Request - State: open - Opened by jburos about 7 years ago

#46 - Adapting to new docker dev environment, reproducible gene lists, and Cibersort comparison figure

Pull Request - State: closed - Opened by maximz about 7 years ago

#46 - Adapting to new docker dev environment, reproducible gene lists, and Cibersort comparison figure

Pull Request - State: closed - Opened by maximz about 7 years ago

#45 - Converted some old notebooks to python3

Pull Request - State: closed - Opened by maximz about 7 years ago

#45 - Converted some old notebooks to python3

Pull Request - State: closed - Opened by maximz about 7 years ago

#44 - Investigate RCC cohort that has bulk RNA-seq of TME and flow sorting data

Issue - State: open - Opened by maximz about 7 years ago - 1 comment

#44 - Investigate RCC cohort that has bulk RNA-seq of TME and flow sorting data

Issue - State: open - Opened by maximz about 7 years ago - 1 comment

#43 - How to estimate uncertainty at each level of the immune cell type hierarchy?

Issue - State: closed - Opened by maximz over 7 years ago - 3 comments

#43 - How to estimate uncertainty at each level of the immune cell type hierarchy?

Issue - State: closed - Opened by maximz over 7 years ago - 3 comments

#42 - Out-of-sample synthetic mixtures tests and visual investigation of correlation matrix

Pull Request - State: closed - Opened by maximz over 7 years ago - 1 comment

#42 - Out-of-sample synthetic mixtures tests and visual investigation of correlation matrix

Pull Request - State: closed - Opened by maximz over 7 years ago - 1 comment

#41 - Remove data leakage in synthetic mixture tests

Issue - State: open - Opened by maximz over 7 years ago

#41 - Remove data leakage in synthetic mixture tests

Issue - State: open - Opened by maximz over 7 years ago

#40 - Try variational inference models

Issue - State: open - Opened by maximz over 7 years ago

#40 - Try variational inference models

Issue - State: open - Opened by maximz over 7 years ago

#39 - Plan how to model stromal and tumor cell content in mixtures

Issue - State: open - Opened by maximz over 7 years ago

#39 - Plan how to model stromal and tumor cell content in mixtures

Issue - State: open - Opened by maximz over 7 years ago

#38 - Biokepi

Pull Request - State: closed - Opened by e5c over 7 years ago

#38 - Biokepi

Pull Request - State: closed - Opened by e5c over 7 years ago

#37 - Abstract for Penn math/bio symposium

Issue - State: open - Opened by e5c over 7 years ago

#37 - Abstract for Penn math/bio symposium

Issue - State: open - Opened by e5c over 7 years ago

#36 - Modify MSOS data.py to pull data from nfs-pool, not the g bucket

Issue - State: open - Opened by e5c over 7 years ago

#36 - Modify MSOS data.py to pull data from nfs-pool, not the g bucket

Issue - State: open - Opened by e5c over 7 years ago

#35 - Create setup.py, fix requirements.txt

Issue - State: open - Opened by e5c over 7 years ago
Labels: bug

#35 - Create setup.py, fix requirements.txt

Issue - State: open - Opened by e5c over 7 years ago
Labels: bug

#34 - Remove kernelspec from ipynbs in `master` branch

Issue - State: open - Opened by e5c over 7 years ago

#34 - Remove kernelspec from ipynbs in `master` branch

Issue - State: open - Opened by e5c over 7 years ago

#33 - Review Dana Pe'er's model for scRNA seq using BISCUIT

Issue - State: open - Opened by jburos over 7 years ago - 1 comment

#33 - Review Dana Pe'er's model for scRNA seq using BISCUIT

Issue - State: open - Opened by jburos over 7 years ago - 1 comment

#32 - model5 negative parameter error

Issue - State: open - Opened by e5c over 7 years ago - 7 comments
Labels: bug

#32 - model5 negative parameter error

Issue - State: open - Opened by e5c over 7 years ago - 7 comments
Labels: bug

#31 - strange pystan error when running model7

Issue - State: open - Opened by jburos over 7 years ago

#31 - strange pystan error when running model7

Issue - State: open - Opened by jburos over 7 years ago

#30 - Error message when running model7 with no cell-level features

Issue - State: open - Opened by jburos over 7 years ago - 1 comment
Labels: bug

#30 - Error message when running model7 with no cell-level features

Issue - State: open - Opened by jburos over 7 years ago - 1 comment
Labels: bug

#29 - Model/stancache working properly?

Issue - State: closed - Opened by e5c over 7 years ago - 1 comment

#29 - Model/stancache working properly?

Issue - State: closed - Opened by e5c over 7 years ago - 1 comment

#28 - compare single-origin model inference to known tool output

Issue - State: open - Opened by jburos almost 8 years ago

#28 - compare single-origin model inference to known tool output

Issue - State: open - Opened by jburos almost 8 years ago

#27 - add adjustment for sample source (batch and/or project)

Issue - State: open - Opened by jburos almost 8 years ago

#27 - add adjustment for sample source (batch and/or project)

Issue - State: open - Opened by jburos almost 8 years ago

#26 - execute all notebooks in single origin samples

Issue - State: open - Opened by jburos almost 8 years ago - 1 comment

#26 - execute all notebooks in single origin samples

Issue - State: open - Opened by jburos almost 8 years ago - 1 comment

#25 - scale up fitting & testing of models (maybe using ketrew)

Issue - State: closed - Opened by jburos almost 8 years ago - 1 comment
Labels: duplicate

#25 - scale up fitting & testing of models (maybe using ketrew)

Issue - State: closed - Opened by jburos almost 8 years ago - 1 comment
Labels: duplicate

#24 - simulate data according to our model

Issue - State: open - Opened by jburos almost 8 years ago - 3 comments

#24 - simulate data according to our model

Issue - State: open - Opened by jburos almost 8 years ago - 3 comments

#23 - Ketrewize Stan model training

Issue - State: open - Opened by e5c almost 8 years ago

#23 - Ketrewize Stan model training

Issue - State: open - Opened by e5c almost 8 years ago

#22 - Schedule formal model review

Issue - State: open - Opened by jburos almost 8 years ago - 2 comments

#22 - Schedule formal model review

Issue - State: open - Opened by jburos almost 8 years ago - 2 comments

#21 - Document current mixture model

Issue - State: open - Opened by jburos almost 8 years ago

#21 - Document current mixture model

Issue - State: open - Opened by jburos almost 8 years ago

#20 - Evaluate sequencing vendors for RNA isolated at MUSC and Sinai

Issue - State: open - Opened by hammer almost 8 years ago - 3 comments

#20 - Evaluate sequencing vendors for RNA isolated at MUSC and Sinai

Issue - State: open - Opened by hammer almost 8 years ago - 3 comments

#19 - Generate data at ISMMS

Issue - State: open - Opened by hammer almost 8 years ago - 2 comments

#19 - Generate data at ISMMS

Issue - State: open - Opened by hammer almost 8 years ago - 2 comments

#18 - Name for this project/tool

Issue - State: open - Opened by jburos almost 8 years ago - 6 comments

#18 - Name for this project/tool

Issue - State: open - Opened by jburos almost 8 years ago - 6 comments

#17 - How to adjust for transcript length

Issue - State: open - Opened by hammer almost 8 years ago - 1 comment

#17 - How to adjust for transcript length

Issue - State: open - Opened by hammer almost 8 years ago - 1 comment

#16 - Try models using selected sets of genes

Issue - State: open - Opened by hammer almost 8 years ago - 2 comments

#16 - Try models using selected sets of genes

Issue - State: open - Opened by hammer almost 8 years ago - 2 comments

#15 - Look into using alternate metrics

Issue - State: open - Opened by hammer almost 8 years ago - 2 comments

#15 - Look into using alternate metrics

Issue - State: open - Opened by hammer almost 8 years ago - 2 comments

#14 - Generate data at MUSC

Issue - State: open - Opened by hammer almost 8 years ago - 57 comments