James Ashmore

MACS2 stalls pre-computing pvalue-qvalue table..

10

Hello, MACS2 stalls at the following line: ``` #3 Pre-compute pvalue-qvalue table... ``` I have two BAM files, one converted to BAM from Bowtie2 output and the other which has...

What is the difference between fate probability and ancestor probability?

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Sorry for the naive question, but what is the difference between fate probabilities and the ancestor probabilities derived from trajectories? I assume cells which show high fate probabilities for a...

Preparation of expression matrix

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I am a bit confused about the "preparation of expression matrices" section in the STAR methods of the optimal transport paper. You define three different expression matrices: the UMI matrix,...

Set colour scale limits in reduced dimension panel

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**Is your feature request related to a problem? Please describe.** I have z-scores in my column data which I would like to display in the reduced dimension panel. Sometimes the...

**Is your feature request related to a problem? Please describe.** Per the recommendations in this [article](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006907#sec007) by Nguyen et al (2019). "The height-to-width ratio of a PCA plot should be...

I use Intervene in a computational pipeline to check overlaps from multiple BED files. The command I use is: `intervene pairwise --input --compute jaccard --output ` Sometimes one of the...

Methods for splitting SingleCellExperiment objects

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Is there scope to define a splitColData and splitRowData methods for the SingleCellExperiment class? I am working with a rather large SingleCellExperiment object and I often find myself needing to...

Slingshot method does not detect groups_id and dimred prior information

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I am trying to run Slingshot (latest master build) with prior information (groups_id and dimred) however neither of these arguments are detected by the relevant method: ``` mod

Slingshot requires cluster labels and a dimensionality reduction to run trajectory analysis. These are computed internally within the ti_slingshot method. Would it be possible to add functionality to the method...

For certain histone modifications, [ENCODE uses the gappedPeak representation.](https://sites.google.com/site/anshulkundaje/projects/encodehistonemods) Right now IDR doesn't support using gappedPeak files - is there a workaround for this? For example, converting a gappedPeak file...