Zepeng (Phoenix) Mu

version 1.12 call only outputs GT

1

Hi, I'm running the same command with bcftools v1.9 and v1.12: ```sh bcftools mpileup Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz -I -E -a 'FORMAT/DP' -r 22 --max-depth 1000 -T ALL.chr22.sites.vcf.gz smp_possorted_nodup.bam -Ou | bcftools call...

Different group labels for the same predicted cell in integrated scRNA

4

Hi, I have noticed strange behavior when adding GeneIntegrationMatrix. I have posted a Discussion several months ago but I think it might be useful to open an Issue as well....

forcerun has no effect

1

Using snakemake 7.14.0, it seems that `forcerun` has no effect unless I also specify the output files in `rule all`. But using previous version, specify intermediate output files is not...

`System command 'R' failed` for any packages

2

```r > remotes::install_github("stephenslab/mashr", build_vignettes = F) Downloading GitHub repo stephenslab/mashr@HEAD ✔ checking for file ‘/tmp/Rtmp04xv01/remotes57651587d912/stephenslab-mashr-e482cf2/DESCRIPTION’ (362ms) ─ preparing ‘mashr’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ running ‘cleanup’...

Make HLA supplementary file

7

Hi, I'm wondering how I can make a `--quilt_hla_supplementary_info_file` for hg19. I guess I can liftOver the file provided in the Github repo, but I hope to add more genes,...

error: expected ')' before 'PRId64'

3

Hi, I encountered this error when trying to install popscle. My C and CXX compiler version are 9.3.0. HTSlib 1.10.2. This error seems to be related to GNU version? But...

Hello, I used bamCoverage with RPKM normalization to get bigwig files. I then used `pyBigWig.values()` function to view bigwig files in a given genomic region. I noticed all the non-zero...

`julia_setup` erorr in Rstudio

1

Hi, I'm encountering this error in `julia_setup`: ```r > j

Uninformative MemoryError message

5

Hi, when I'm running vireo, I encountered this error: ``` numpy.core._exceptions.MemoryError: Unable to allocate 178. MiB for an array with shape (1939760, 4, 3) and data type float64 ``` This...

Hi, I am running the example code but got the error: ``` Error in FUN(X[[i]], ...) : object 'values.radar' not found ``` How can I resolve this? Thanks