User: layal8785

gravatar for layal8785
layal87850
Reputation:
0
Status:
New User
Last seen:
1 year, 11 months ago
Joined:
2 years, 5 months ago
Email:
l********@gmail.com

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

This helps us discourage the inappropriate use of our site.

Posts by layal8785

<prev • 5 results • page 1 of 1 • next >
1
vote
0
answers
773
views
0
answers
DEXseq plot, determin the EU Fold change
... In "plotDEXseq" function, we can provide the FDR and other few arguments as normalized counts, names, ...  The  significant differential used exon  shows as a red bar. but I want to visualize as significant just the exons which passed my adjusted P-value and log2FoldChange thresholds for example I ...
dexseq plotdexseq written 2.1 years ago by layal87850
0
votes
1
answer
740
views
1
answers
Comment: A: genes symbol in RangedSummarizedExperiment object and add GRangesList to DESeqDa
... I created the count matrix from featureCount FC_countreads <- featureCounts(files="pathes to 12bam files", isPairedEnd=TRUE, annot.ext= "pathsToGeneAnnotation/Mus_musculus.GRCm38.86.gtf", isGTFAnnotationFile=TRUE, GTF.featureType="ex ...
written 2.4 years ago by layal87850
0
votes
1
answer
740
views
1
answer
genes symbol in RangedSummarizedExperiment object and add GRangesList to DESeqDataSet object in DESeq2
... I hope I can get clear answer, because I didn't come here to ask till I've struggled for few days. 1) I wanted to get the fpkm counts from the DESeqDataSet object I created it from DESeqDataSetFromMatrix,but a column basepairs is not present in mcols(dds) (mcols of DESeqDataSet object after applyin ...
deseq2 grangeslist rangedsummarizedexperiment written 2.4 years ago by layal87850
0
votes
3
answers
8.3k
views
3
answers
Comment: C: DESeq2: add annotations (from data frame) to DESeqDataSet
... Hi Micheal I think the gene Symbol when we use DESeqDataSetFromMatrix, it is somehow easy compare the unclear way how to deal with the SummarizedExperiment object when we construct the count matrix from featcherCounts we add the argument (GTF.attrType="gene_name") I would like you to answer our q ...
written 2.4 years ago by layal87850
0
votes
1
answer
707
views
1
answer
warning in makeTxDbFromGFF
... The warning in creating TxDb: gtffile <- file.path("PATH/Mus_musculus.GRCm38.86.gtf") txdb <- makeTxDbFromGFF(gtffile, format="gtf") Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Warning messages: 1: Na ...
genomicfeatures written 2.4 years ago by layal87850 • updated 2.4 years ago by James W. MacDonald50k

Latest awards to layal8785

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: 211 users visited in the last hour