Tim Triche, Jr.

Installation will fail otherwise in the event user does not have plot3D already installed.

$ operator

6

I wrote a one-liner to add $ support for igraph. Is this reasonable? ``` `$.igraph`

Large SCEs (~ 1 million cells) break H5AD export due to dependency on cholmod_dense.c

1

Granted, the whole point of scanpy is that it can handle these sorts of things... ```# import h5ad to SCE library(zellkonverter) merged

[fetch_refseq:40] Error, cannot retrieve reference chr1:0-0.

16

After marking dupes, the following biscuit pileup -q 16 -r hg19.fa -i WGBS_$SAMPLE.mkdups.hg19.bam -o WGBS_$SAMPLE.mkdups.hg19.vcf fails on a number of samples (4/6, not all though). Is there a straightforward way...

I'll be damned if I'm 100% sure, but it seems that the assertion of unit width only applies to the epistate number (1 or 2) and the Waston/Crick strand (+/-),...

biscuit asm fails on generated epiread files

3

Compiled with debug symbols and run under gdb... ``` gdb -q --args ./biscuit asm epiread.txt Reading symbols from ./biscuit...done. (gdb) b main_asm Breakpoint 1 at 0x453853: file src/asm_pairwise.c, line 91....

The existing (and well circulated) example of inlining a CppBugs run into R via Rcpp is http://www.mail-archive.com/[email protected]/msg00825.html An updated version with eg. LDA, a Dirichlet process mixture model, or an...

Small differences in derived txomes relative to reference txome (possible?)

1

Not sure if this is possible/practical at scale but it would seem that if you know the differences between transcriptome versions (i.e. minimum sequence needed to test for say ENS92...

genome reference assembly extraction from variants/reads objects?

4

One of the handy defaults in Bioconductor GRanges/VRanges objects is a slot for the genome (reference assembly) of each chromosome (should all be the same for any sane object, of...

Example code motivating seqlevelsStyle() patch

1

Per #15 and ensuing blahblah, here's the unvarnished code. If it breaks, you get to keep the pieces. :-) ``` R library(GoogleGenomics) ## ## may need to do this interactively:...