User: Mthabisi Moyo

gravatar for Mthabisi Moyo
Reputation:
10
Status:
New User
Location:
Last seen:
6 days, 15 hours ago
Joined:
2 years, 8 months ago
Email:
m***************@u.northwestern.edu

Posts by Mthabisi Moyo

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answers
77
views
1
answers
Comment: C: goseq: Formatting category list for use with goseq
... Thank you, this was very helpful. As your example demonstrates, I did not have to convert the ontology/ category lists to ensembl IDs. It was sufficient to just convert the differentially expressed gene set to entrez IDs. As far as the inconsistency between entrez IDs and ensembl IDs, I had noticed ...
written 27 days ago by Mthabisi Moyo10
1
vote
1
answer
77
views
1
answer
goseq: Formatting category list for use with goseq
... I am using goseq for category testing of differentially expressed genes in my RNA-seq data sets and I wanted to extend it to categories other than the GO categories. Specifically, I wanted to make use of the molecular signatures database (MSigDB). To be clear, I am not trying to do a ranking approac ...
goseq category test written 28 days ago by Mthabisi Moyo10 • updated 27 days ago by James W. MacDonald48k
0
votes
1
answer
77
views
1
answer
Counting exonic and intronic reads for differential gene expression
... I have always assumed that reads mapping to exons are used as the input for differential gene expression analysis in DESeq2 (and other DGE analysis packages) primarily because poly(A) capture protocols are favored over total RNA prep protocols, resulting in a majority of sequenced reads being exonic ...
deseq2 intron written 5 weeks ago by Mthabisi Moyo10 • updated 5 weeks ago by Malcolm Cook1.5k
0
votes
0
answers
78
views
0
answers
Gviz: plotting multiple data tracks with the same y-axis limit using Gviz
... I am using Gviz to plot H3K27Ac and RNAPII ChIP-seq data for two experimental conditions, Wt and KO: WT_H3K27Ac <- DataTrack(range = '/path/to/WT-H3K27Ac.bw', type = "histogram", window = -1, name = "WT H3K27Ac", genome = "GRCh38", col.histogram = "black", fill.histogram = "black") KO_H3K27Ac &l ...
gviz gviz-package written 10 weeks ago by Mthabisi Moyo10
1
vote
1
answer
130
views
1
answer
ntop parameter in plotPCA(). DESeq2
... Given that the PCA plot is likely to change somewhat depending on the number of genes you decide to specify with the ntop parameter, are there any recommendations on how to best set this value besides arbitrarily setting it at the default of 500/1000? Could including all genes have a negative effect ...
deseq2 written 4 months ago by Mthabisi Moyo10 • updated 4 months ago by Michael Love19k
0
votes
1
answer
99
views
1
answer
Blocking factors for differential binding analysis with DiffBind
... I have performed ChIP-seq for multiple transcription factors on samples from multiple patients. All ChIPs for each patient where sequenced on different sequencing runs (i.e. TF1, TF2, TF3 for patient 1 was on one flowcell and  TF1, TF2, TF3 for patient 2 was on a separate flowcell etc). I am looking ...
diffbind written 4 months ago by Mthabisi Moyo10 • updated 20 days ago by Rory Stark2.6k
0
votes
0
answers
124
views
0
answers
Changing box plot font sizes for axes and labels in DiffBind
... I have been trying to change font sizes for my box plots in DiffBind: dba.plotBox(x, th = 0.05, pars = list(cex.axis=1.5, cex.main=2, cex.lab=1.5)) I have also tried the following variation: dba.plotBox(x, th = 0.05, cex.axis=1.5, cex.main=2, cex.lab=1.5) I assumed that these arguments would b ...
diffbind written 4 months ago by Mthabisi Moyo10
0
votes
1
answers
411
views
1
answers
Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... I missed that, thanks for the catch! Deleting the .AnnotationHub folder cleared the cache and did the trick. I ran ensembldb using both the EnsDb I made from the Ensembl GRCh38 .gtf annotation file (v90) and the one I downloaded through AnnotationHub and both worked well. The only point I would mak ...
written 13 months ago by Mthabisi Moyo10
0
votes
1
answers
411
views
1
answers
Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... I deleted the .AnnotationHub folder in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/AnnotationHub and the result is unchanged. I still get 0 queries after reinstalling AnnotationHub database using Biocinstaller. Mthabisi   ...
written 13 months ago by Mthabisi Moyo10
0
votes
1
answers
411
views
1
answers
Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... Thanks for the feedback! 1) I was able to construct the package using Ensembl 90 without a problem: >gtffile <- "/user/Downloads/Homo_sapiens.GRCh38.90.gtf.gz" > DB <- ensDbFromGtf(gtffile) Importing GTF file ... OK Processing metadata ... OK Processing genes ... Attribute availabi ...
written 13 months ago by Mthabisi Moyo10

Latest awards to Mthabisi Moyo

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 2.2.0
Traffic: 371 users visited in the last hour