cohorts

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From @iskandr re https://github.com/hammerlab/mhctools/pull/86: > Followup to mhctools PR, a much smaller change to make Topiary work: https://github.com/hammerlab/topiary/pull/66 > The only API changes that should matter to you are `epitope_lengths`...

tavinathanson

Support stratified cohorts, as a way to combine more than one sample of patients

1

jburos

Do something with epidisco.py

1

@jburos wrote some useful utilities in https://github.com/hammerlab/rcc-analyses/blob/master/analyses/epidisco.py and https://github.com/hammerlab/ovarian-msk-chemo/blob/master/epidisco/epidisco.py (the latter contains some additional utilities, I believe) that we should factor out into public code. One idea is a `discohorts`...

tavinathanson

Per https://github.com/hammerlab/cohorts/pull/179#issuecomment-273334798

tavinathanson

Modify isovar usage from >=3 to >=2 spanning reads

1

Per https://github.com/hammerlab/cohorts/pull/177#discussion_r96321375

tavinathanson

Will require a test BAM.

tavinathanson

Resolve overlap between epidisco and cohorts

7

From @tavinathanson: > I'm fairly unclear right now about how best, when using cohorts, to use epidisco results; for example using epidisco neoepitopes rather than https://github.com/hammerlab/cohorts/blob/master/cohorts/cohort.py#L767 > > One obstacle...

tavinathanson

Currently, regular neoantigens use `topiary` while expressed neoantigens use `isovar` + `mhctools` because `topiary` doesn't use isovar. This depends on `topiary` making use of `isovar`, I think. Related: https://github.com/hammerlab/vaxrank/issues/31

tavinathanson

Add `batch` identifier to cohorts & support estimation of batch effects

1

Would be useful to keep track of `batch` identifiers so we can estimate batch effects as part of standard protocol.

jburos

Support NA PFS or OS

2

Maybe out of scope for this project, but for TCGA data it would be useful to support PFS or OS being set to NaN. Right now, this gives an error...

arahuja