User: Biogeek

gravatar for Biogeek
Biogeek350
Reputation:
350
Status:
Trusted
Location:
Last seen:
4 months, 1 week ago
Joined:
5 years, 9 months ago
Email:
p**********@gmail.com

about me

Posts by Biogeek

<prev • 182 results • page 1 of 19 • next >
0
votes
4
answers
348
views
4
answers
Comment: C: General question about batch effect, read trimming and what to do when the adapt
... Mozart, the paired files are what you use. I just want to confirm with you though...Are they the correct Adaptor sequences that your sequencing was performed with? It may be that the adaptor sequences were removed by the facility, common. As such, very low % of reads will be trimmed.. [Link to Next ...
written 4 months ago by Biogeek350
0
votes
1
answer
156
views
1
answers
Comment: C: gene IDs enrichment in plants
... What sort of data do you want to carry out an enrichment on? Also what plant are you working with, is it a model or a non-model? ...
written 5 months ago by Biogeek350
1
vote
4
answers
348
views
4
answers
Answer: A: General question about batch effect, read trimming and what to do when the adapt
... I'd recommend using BBDUK under the bb tools suite by Brian Bushnell. It has an extensive adapter.fa file containing all publicly available adaptor sequences - just an idea? The amount of times people sue Trimmomatic without the correct adaptor sequence .fa file. Admittedly I also made that mistake ...
written 5 months ago by Biogeek350
0
votes
1
answer
175
views
1
answers
Answer: A: Making a Group Tree using RNA-seq Read Count in R
... Hi Minuate, Can you please specify what sort of 'tree'? Do you mean a heatmap or dendrogram based figure? If so you can use heatmap.2 or pheatmap in R. In conjunction with ggplots2 and other various R modules, you can make some pretty nice diagrams. If that count data is normalised, you can log2 t ...
written 5 months ago by Biogeek350
0
votes
0
answers
260
views
0
answers
Confused with Fishers test for GO enrichment
... Hi, I'm running the fisher.test function in R. My code is: dfx <- input_fishers res1<- NULL for (i in 1:nrow(dfx)){ table1 <- matrix(c(dfx[i,1], dfx[i,2], dfx[i,3], dfx[i,4]), ncol = 2, byrow = TRUE) p1<- fisher.test(table1, alternative = "greater")$p.value res1 ...
fishers input enrichment written 5 months ago by Biogeek350
0
votes
1
answer
222
views
1
answer
Example of gene2cat goseq
... Any examples of the gene2cat input for a non-model organism? I'm working in R. My first column is GO:XXXXXX and my second column is gene ID. Row names are numerical (automatic). To be fair the Vignette and guides aren't so clear considering a lot of people use it for non-model organisms. I'm gettin ...
goseq written 5 months ago by Biogeek350 • updated 5 months ago by cfos4698130
0
votes
3
answers
209
views
3
answers
Comment: C: Split comma seperated list of GO terms into multiple rows and maintain gene iden
... Many thanks for the python version also! ...
written 5 months ago by Biogeek350
0
votes
3
answers
209
views
3
answers
Comment: C: Split comma seperated list of GO terms into multiple rows and maintain gene iden
... Many thanks for the R version! ...
written 5 months ago by Biogeek350
0
votes
3
answers
209
views
3
answers
Comment: C: Split comma seperated list of GO terms into multiple rows and maintain gene iden
... Perfect! This works. Thanks very much! ...
written 5 months ago by Biogeek350
7
votes
3
answers
209
views
7 follow
3
answers
Split comma seperated list of GO terms into multiple rows and maintain gene identifier in each
... I have a tab separated dataset, although the GO terms are comma separated. GENEID1 GO:XXXXX,GO:YYYYYY,GO:ZZZZZZ I want to make it so that the dataset becomes a tab-seperated dataset where each GO term is represented on a new line with the gene identifier: GENEID1 GO:XXXXX GENEID1 ...
gene ontology data manipulation written 5 months ago by Biogeek350 • updated 5 months ago by st.ph.n2.5k

Latest awards to Biogeek

Popular Question 5 months ago, created a question with more than 1,000 views. For RNA-Seq of environmental samples
Popular Question 5 months ago, created a question with more than 1,000 views. For RNA-Seq of environmental samples
Popular Question 5 months ago, created a question with more than 1,000 views. For RNA-Seq of environmental samples
Popular Question 7 months ago, created a question with more than 1,000 views. For RNA-Seq of environmental samples
Popular Question 8 months ago, created a question with more than 1,000 views. For EdgeR filter thresholds
Popular Question 8 months ago, created a question with more than 1,000 views. For EdgeR filter thresholds
Supporter 8 months ago, voted at least 25 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For EdgeR filter thresholds
Popular Question 18 months ago, created a question with more than 1,000 views. For EdgeR filter thresholds
Popular Question 18 months ago, created a question with more than 1,000 views. For curating a viridiplantae database
Popular Question 18 months ago, created a question with more than 1,000 views. For Low number of differentially expressed genes
Popular Question 18 months ago, created a question with more than 1,000 views. For Stand alone Blast annotation with multiple databases
Popular Question 18 months ago, created a question with more than 1,000 views. For Parsing uniprot .dat files
Popular Question 18 months ago, created a question with more than 1,000 views. For Going from BlastX to GO annotation
Popular Question 18 months ago, created a question with more than 1,000 views. For Biological variation within replicate groups, not much DE
Popular Question 18 months ago, created a question with more than 1,000 views. For Can you pool individuals to make 1 biological replicate?
Popular Question 18 months ago, created a question with more than 1,000 views. For Heatmap.2 - flip dendrogram so control group appears on LHS?
Popular Question 18 months ago, created a question with more than 1,000 views. For Time-series or pairwise comparison EdgeR - what's more suited?
Popular Question 18 months ago, created a question with more than 1,000 views. For Annoying STAR aligner problem
Popular Question 18 months ago, created a question with more than 1,000 views. For Alignment of seq reads to a genome, process after STAR?
Popular Question 18 months ago, created a question with more than 1,000 views. For normalized FPKM matrix file EdgeR and GO Mapping
Popular Question 18 months ago, created a question with more than 1,000 views. For Low number of differentially expressed genes
Popular Question 22 months ago, created a question with more than 1,000 views. For Is There Such A Way/ Program To Do This...
Popular Question 22 months ago, created a question with more than 1,000 views. For Weird Outputs With Dynamictrim And Lengthsort On Custom Settings
Popular Question 22 months ago, created a question with more than 1,000 views. For normalized FPKM matrix file EdgeR and GO Mapping

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 793 users visited in the last hour