User: bright602

gravatar for bright602
bright6020
Reputation:
0
Status:
New User
Last seen:
1 year ago
Joined:
1 year, 7 months ago
Email:
b********@me.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by bright602

<prev • 9 results • page 1 of 1 • next >
0
votes
0
answers
227
views
0
answers
How to get the genome distribution in proportion of promoter, 1st exon, other exon, 1st intron, other intron, distal intergenic, etc from a species
... Recently, I am working on annotating the peak files using ChIPseeker. I am wondering is there away to understand the original genome distribution of each categories (promoter, 1st exon,  other exon, 1st intron, other intron, distal intergenic, etc.) from a species? In that case, I could have a basel ...
chipseeker written 13 months ago by bright6020
0
votes
1
answer
477
views
1
answers
Comment: C: enrichMKEGG can not identify the species
... Thanks for reply. I will look into that and have a try.   ...
written 14 months ago by bright6020
0
votes
1
answer
477
views
1
answers
Comment: C: enrichMKEGG can not identify the species
... > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.5 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frame ...
written 14 months ago by bright6020
0
votes
1
answer
477
views
1
answers
Comment: C: enrichMKEGG can not identify the species
... > library(clusterProfiler) > data(geneList, package='DOSE') > de <- names(geneList)[1:100] > yy <- enrichKEGG(de, organism='hsa', pvalueCutoff=0.01) Error in download.KEGG.Path(species) :   'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.h ...
written 14 months ago by bright6020
0
votes
1
answer
477
views
1
answers
Comment: C: enrichMKEGG can not identify the species
... Thanks Guido, I tried to repeat but the same error message still pop out. ...
written 14 months ago by bright6020
0
votes
1
answer
477
views
1
answer
enrichMKEGG can not identify the species
... Hi there, Recently I tried to use enrichMKEGG or enrichKEGG function from clusterProfiler, however, there is an error message stating that Error in download.KEGG.Module(species) :   'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... Even I tried to ...
clusterprofiler written 14 months ago by bright6020 • updated 14 months ago by Guido Hooiveld2.5k
1
vote
1
answer
222
views
1
answer
DiffBind question on adb.contrast
... Hi, I have been trying to use the DiffBind for analyzing my ChIP-seq data; during the dba.contrast step, I came across an error that I show below. > H3K4me3 <- dba.contrast(H3K4me3, H3K4me3$masks$V1, H3K4me3$masks$S1, "V", "S",  minMembers=2) Error in pv.addContrast(pv, group1, group2, name1 ...
diffbind written 15 months ago by bright6020 • updated 15 months ago by Rory Stark2.8k
0
votes
0
answers
393
views
0
answers
Error using the makeTxDbFromGFF
... Hi, I came across an error when building the TxDb from GFF as follow: txdb <- makeTxDbFromGFF(gfffile, format="gff") Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Error in .get_cds_IDX(type, phase) :   the " ...
maketxdbfromgff written 19 months ago by bright6020
0
votes
1
answer
457
views
1
answer
Error with makeTxDbFromBiomart in GenomicFeatures package
... Hi there, I was trying to build the txdb file using the makeTxDbFromBiomart, however, I came across with an error. The command I typed was : dicty_txdb <- makeTxDbFromBiomart(biomart="protists_mart", dataset="ddiscoideum_eg_gene", ...
genomicfeatures written 19 months ago by bright6020 • updated 19 months ago by Hervé Pagès ♦♦ 14k

Latest awards to bright602

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 110 users visited in the last hour