Jeremy
Jeremy
I've noticed a few problems with the Seurat3 FeaturePlot function that I wanted to provide feedback on: 1) When using the split.by option, FeaturePlot correctly separates according to the factor...
Hello! When creating a plot with a lot of RowSideColors, the RowSideColors legend tends to get a bit unwieldy and can overlap with the actual legend. I've found that setting...
Thanks again for a great package. Would be really useful to be able to easily add freestyle text annotations using e.g., grid coordinates in a manner similar to ggplot2's "annotation".
Beautiful package-- thanks so much for making this! I just figured out that the dendrogram heights can be controlled by setting yr.plot.size and yt.plot.size; however, things like yr.line.col and yr.line.size...
It is currently possible for sequences that are missing required parts of certain gene segments to evade the parts of our pipeline that filter out of frame TCRs. For instance:...
I think currently we exclude all out of frame CDR3s from any part of the analysis after sequence parsing. It's good to exclude these from analysis since they are non-functional,...
The use of --no_probabilities is currently limited by the fact that compute_probs imports tcr_rearrangement_new.py or tcr_rearrangement.py (both directly and also through the importing of tcr_sampler.py). the _rearrangement_ scripts have functions...
"The Windows API imposes a maximum filename length such that a filename, including the file path to get to the file, can't exceed between 255-260 characters." Filenames that violate this...
Hello, I've been running SCENIC in R successfully but running into problems with exporting the results in loom format, which is the format utilized in the tutorials for downstream analyses...
Hi, I've been unable to use the --coverage subarg of output without generating an error: ``` terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_M_construct null not valid Aborted...