Dan Li

`hgd_browse()`: This site can’t be reached

2

Hello: When I run the code: ```r library(httpgd) library(unigd) hgd() hgd_browse() ``` How should I fix the "This site can’t be reached" error in Google Chrome?  Thanks

Why the 4th column of bedgraph file values are E0, E1 and E2? What is the meaning of these values?

1

Hello: I thought the 4th column of `bedgraph` file should be a digital number which is the value of the region. But for the `HMMRATAC` output, why the 4th column...

Hello, I run ``` samtools view -H C1.FINAL.BAM | perl -ne 'if(/^@SQ.*?SN:(\w+)\s+LN:(\d+)/){print $1,"\t",$2,"\n"}' > genomeinfo/C1.FINAL.BAM java -jar ~/HMMRATAC_V1.2.10_exe.jar -b C1.FINAL.BAM -i C1.FINAL.BAM.bai -g genomeinfo/C1.FINAL.BAM ``` But got this error: ```...

`Error in GenomicRangesList(features = feat, flanks = flanks) : could not find function "GenomicRangesList"`

2

Hello: How should I solve this error: ```r library(GenomicRanges) library(genomation) cpg.file=system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit") cpg.obj=readFeatureFlank(cpg.file, feature.flank.name=c("CpGi","shores")) ``` ```r Error in GenomicRangesList(features = feat, flanks = flanks) : could not...

Error in validObject(.Object) : invalid class "ScoreMatrix" object: superclass "mMatrix" not defined in the environment of the object's class

2

Hello How should I solve this problem? ```r library(genomation) transcriptFile=system.file("extdata", "refseq.hg19.chr20.bed", package="compGenomRData") feat=readTranscriptFeatures(transcriptFile, remove.unusual = TRUE, up.flank = 500, down.flank = 500) prom=feat$promoters # get promoters from the features #...

`phonograph.cluster()` function doesn't seem to work correctly on Windows Subsystem for Linux

12

Hi I run this PhenoGraph tutorial "tutorial_pbmc3k.ipynb" But the “phonograph.cluster()” function can’t successfully calculate the communities, all the communities are zeros. But there is no error or warning. Is there...

Error in `map()`: ℹ In index: 1. Caused by error: ! The 'image' argument is not a magick image object.

2

Hello Mitchell When I run the code on the website `https://www.mitchelloharawild.com/blog/hexwall/`, there is an error: ``` > sticker_rows % + map(~ stickers[.x] %>% + exec(c, .) %>% + image_append) Error...

Error in polygon(polar2Cartesian(d2), ...) : plot.new has not been called yet

1

Hi: Thanks for the nice package! When I run the code in chapter 1: ``` set.seed(999) n = 1000 df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE), x =...

Why the `simplifyGOFromMultipleLists(lt)` has less clusters than the components?

1

Why the `simplifyGOFromMultipleLists(lt, padj_cutoff = 0.01)` has less clusters than the components? How can I maintain all the clusters of every component? And how to show the word cloud of...

`runAme(sequences, control = "shuffle", evalue_report_threshold = 30)` get `FATAL: Template does not contain data section`

4

Hello: I run the example codes in the `README`: ```r check_meme_install() ``` ```bash checking main install ✔ /home/dan/meme/bin checking util installs ✔ /home/dan/meme/bin/dreme ✔ /home/dan/meme/bin/ame ✔ /home/dan/meme/bin/fimo ✔ /home/dan/meme/bin/tomtom ✔...