Ryan Corces

Does nf-core/atacseq apply an offset to each ATAC-seq fragment?

3

Does the pipeline apply the standard +4/-5 offsets to aligned reads to account for the precise Tn5 binding site? I have not been able to find this in the documentation...

Originally, peak sets do not have a `name` column. This means that when `getFeatures()` is called, it returns `NULL` because no `name` column is present. This makes it impossible to...

addArchRAnnotations() is incompatible with getPositions()

1

### Discussed in https://github.com/GreenleafLab/ArchR/discussions/1405 Originally posted by **rojinsafavi** April 27, 2022 Not sure if this is a bug, or if I am missing something here. I added "EncodeTFBS": ```projHeme2

Addressing https://github.com/GreenleafLab/ArchR/issues/1379 Issues with `projectBulkATAC()` when `dimsToUse` has been set.

.testMarkerSC() failing when mean1 and/or mean2 is NA during call to getMarkerFeatures()

3

### Discussed in https://github.com/GreenleafLab/ArchR/discussions/1319 Originally posted by **wuv21** March 3, 2022 Hi! Been running into an issue similar to #562 and #483 with the same error output, but I have...

I'm not sure if this is the expected behavior but I dont seem to be getting files populated in the corresponding alias folders when building a refgenie fasta asset. Specifically,...

Dev module score

1

Addressing https://github.com/GreenleafLab/ArchR/issues/1631

Harmony installation has changed

1

Harmony is no longer recommended to be installed with devtools and is now available in CRAN. We need to update the `installExtraPackages()` function and the `DESCRIPTION` file for ArchR to...

test pull request for comparing changes

predictionCutoff parameter in addPeak2GeneLinks

1

### Discussed in https://github.com/GreenleafLab/ArchR/discussions/1814 Originally posted by **RegnerM2015** January 19, 2023 Hi @rcorces and @jeffmgranja , I was looking at the source code for `addPeak2GeneLinks` and the use of predictionCutoff:...