I-Hsuan Lin

This PR adds support for using `nudge_x` and `nudge_y` in `geom_parallel_sets_labels` when creating parallel sets diagrams. It is especially useful when the labels are too long to fit inside the...

"bcf_fmt_array" error

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Hi I am using `vt decompose -s -d` on a VCF file and encountered an "Unexpected type 0" error without produced the resulting VCF ``` decompose v0.5 options: input VCF...

non-existent physical address

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Data dimension is: [1] 1221 5000 Error message as below: NMF algorithm: 'brunet' Multiple runs: 100 Mode: parallel (25/32 core(s)) **\* caught bus error *** address 0x2b24518ef000, cause 'non-existent physical...

This PR changes how some functions deal with sequential and parallel processes. Following the suggestion in #424 and discussion in #140 regarding the missing `future.seed` setting, I dropped the detection...

Based on the current `netAnalysis_computeCentrality` function, the `prob` values are adjusted if `pval` did not meet the `thresh`, i.e. set to 0 in L206. https://github.com/sqjin/CellChat/blob/418b660aa896758a6a7858a443c56ffcb522c672/R/analysis.R#L201-L208 However, `pval` is only provided...

This PR (1) resolve the issue with duplicated `Heatmap` object name when joining 2 or more `Heatmap` objects created by the `netVisual_heatmap` function, by create a unique `ht.name` name and...

~~This PR converts numeric matrices from the `Matrix` package to (R base) matrices to resolve error that arises when manipulating R base matrices with non-R-base matrices. This seem to become...

Problem with mixed DelayedMatrix & dgCMatrix data type

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I have a list of `SingleCellExperiment` objects from 10X and non-10X experiments, and the `counts` and `logcounts` assays have a mixture of `DelayedMatrix` (10X) & `dgCMatrix` (non-10X) data types. In...

Allow more than 1 filter.identity level in 'clonalNetwork()'

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Not sure if this is the behaviour you would like to add to the `clonalNetwork` function. This PR allow the `filter.identity` to accept one or more identity levels, so that...

Error: munmap_chunk(): invalid pointer: xxxxxx

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I build squid from source and tried it on one of my sample, but encountered an error and it aborted: ``` $ ./squid-1.0/bin/squid -b Aligned.sortedByCoord.out.bam -c Chimeric.bam -G 1 -CO...