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Davide Cittaro dawe Milan Bioinformartist

theislab/scanpy_usage 48

Scanpy use cases.

dawe/schist 17

An interface for Nested Stochastic Block Model for single cell analysis

dawe/scTips_Twitter 2

Some random code about single cell stuff to share with my Tweeps

dawe/scatACC 1

Things needed for custom scATAC analysis

dawe/schist-notebooks 1

Some example notebooks for scNSBM package

dawe/anndata 0

Annotated data matrix.

dawe/awesome-single-cell 0

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

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issue commentdawe/schist

Remove `unknown` if `use_best` in label transfer

Addressed in 138fd3bd5438ff977ba208ba5ff75de84395d9ff

dawe

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issue closeddawe/schist

Remove `unknown` if `use_best` in label transfer

When scs.tl.label_transfer is issued with use_best=True, unknown label is present in transferred annotations, although it won't be used. It could be better to remove it.

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Cittaro Davide

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remove unused categories when label transfer

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figure with wrong colors

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typo in docs

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change figure size in tutorials

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updated images

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added discussion on unknonw cells

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Done with transfer docs

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Cittaro Davide

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reduced image dimensions

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issue openeddawe/schist

Remove `unknown` if `use_best` in label transfer

When scs.tl.label_transfer is issued with use_best=True, unknown label is present in transferred annotations, although it won't be used. It could be better to remove it.

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minor changes in docs

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Update meta.yaml Update for version 0.7.13

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Davide Cittaro

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Merge pull request #10 from dawe/master Update meta.yaml

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PR merged conda-forge/schist-feedstock

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Update meta.yaml

Update for version 0.7.13

<!-- Thank you for your pull request. Below are a few things we ask you kindly to self-check before getting a review. Remove checks that are not relevant. --> Checklist

  • [X] Used a personal fork of the feedstock to propose changes
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Update meta.yaml

Update for version 0.7.13

<!-- Thank you for your pull request. Below are a few things we ask you kindly to self-check before getting a review. Remove checks that are not relevant. --> Checklist

  • [X] Used a personal fork of the feedstock to propose changes
  • [ ] Bumped the build number (if the version is unchanged)
  • [X] Reset the build number to 0 (if the version changed)
  • [ ] Re-rendered with the latest conda-smithy (Use the phrase <code>@<space/>conda-forge-admin, please rerender</code> in a comment in this PR for automated rerendering)
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Update meta.yaml Update for version 0.7.13

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Merge pull request #9 from dawe/master Changed tests

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created tagdawe/schist

tagv0.7.13

An interface for Nested Stochastic Block Model for single cell analysis

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Cittaro Davide

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inital work on label transfer

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working on LT

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Cittaro Davide

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Initial complete label transfer function

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Cittaro Davide

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everything works except for neighbors

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Cittaro Davide

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apparently you cannot specify "neighbors" as key for scanpy.pp.neighbors

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Cittaro Davide

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Also transfer colors if any

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Cittaro Davide

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Use gray for unknonw

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Cittaro Davide

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Use gray for unknonw

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final checks

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issue closedcaleblareau/mgatk

Integrating multiple data

Hello, I am applying mgatk on several datasets and at a certain point I will need to integrate them. Given that the same cell barcode can be in different experiments, I was thinking I could concatenate the rds objects so that every cell gets a unique name across multiple datasets. Is this legit for downstream analysis? I thought I could then perform a single run of variant calling on the merged dataset. I admit I'm not proficient with R, so any hint on how to merge multiple SummarizedExperiment objects is much appreciated :-) Another question that comes after integration is how to evaluate the similarities among cells. Once variants have been identified (and filtered), would it be appropriate to calculate distances on the allele_frequency values in the data slot?

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dawe

issue commentcaleblareau/mgatk

Integrating multiple data

Thanks, I have solved with cbind() and changing colnames so that they match names in AnnData I am using.

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style in docs

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updated citation

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issue commentvtraag/leidenalg

python-igraph requirements not resolved

Hello, I'm having difficulties in building it from source. Anyhow, a simple conda environment such as

conda create -c conda-forge -n leidentest
conda activate leidentest
conda install leidenalg
pip check

raises the same error, so it has nothing to do with scanpy dependencies

dawe

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issue closeddawe/schist

Broken docs

After small code refactoring in 0.7.12 docs are broken

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