User: Biogeek

gravatar for Biogeek
Biogeek280
Reputation:
280
Status:
Trusted
Location:
Last seen:
4 months, 2 weeks ago
Joined:
4 years, 7 months ago
Email:
p**********@gmail.com

about me

Posts by Biogeek

<prev • 145 results • page 1 of 15 • next >
0
votes
0
answers
120
views
0
answers
Conditional reciprocal blast confusion
... Dear all, I have 2 assemblies. A de novo assembly and a draft genome assembly of an organism. My aim is to confirm that specific genes of the de novo do in fact appear in the draft genome. I will then design primers around the best match obtained form the CRB analysis. I am using crb-blast: https: ...
crb-blast written 4 months ago by Biogeek280
0
votes
2
answers
218
views
2
answers
QTL /linkage trait mapping
... Hey guys, Quick and basic question: I'm on for advancing my skills in bioinformatics, having specialized in transcriptomics for a few years now. I want to delve into QTL linkage mapping in plants. Any good sources to learn from/ complete some tutorials/ practicals? Many thanks for any advice/ s ...
qtl / linkage trait mapping written 5 months ago by Biogeek280 • updated 5 months ago by andrew.j.skelton735.1k
0
votes
2
answers
1000
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... Sorry for being ignorant. I'm unsure how I can feed the above hclustfun into my code. Can you explain how I incorporate that into heatmap.2(....)?Thanks. ...
written 8 months ago by Biogeek280
0
votes
2
answers
1000
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... heatmap.2(lc2, col=colfunc(200),Colv= F, main = "Sample",dendrogram = "both", scale = "none", trace = "none", keysize = 1.0, key.ylab = NA, density.info = "none",key.xlab = "Z-score", labRow = "", breaks = seq(-2, 2, length.out = 201))) My code above, is there a way to do this in that? I'm just usi ...
written 8 months ago by Biogeek280
0
votes
2
answers
1000
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... I will see what I can do. Would it matter if I didn't provide the top dendrogram (Vcol = FALSE) . That command allows me to have control on LHS but just no dendrogram. ...
written 8 months ago by Biogeek280
0
votes
2
answers
1000
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... Have tried these methods, but no luck, Them methods seem to only adjust the rows around? The closest I have got is feeding Vcol = (4,5,6,1,2,3), however, the upper dendrogram becomes flat and doesn't offer any insight into similarity of samples. ...
written 8 months ago by Biogeek280
0
votes
2
answers
1000
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... Hey mate, I tried Colv but it omits the upset dendogram. Would prefer to keep it o show the distances/ similarity. When you say feed it a vector can you elaborate? I give heatmap.2 a matrix of values. Even if I reorder the matrix columns, it still puts the heatmap as is. 😞 ...
written 9 months ago by Biogeek280
4
votes
2
answers
1000
views
2
answers
Heatmap.2 - flip dendrogram so control group appears on LHS?
... I am wanting to flip the dendrogram above my heatmap so that the SC group appears on the left of the heatmap and the IO group appears on the right as opposed to the left. Is there anyway I can do this without removing the dendrograms? The SC is the control group and as such it seems logical that it ...
R heatmap written 9 months ago by Biogeek280 • updated 9 months ago by e.rempel660
0
votes
1
answer
593
views
1
answer
Easier way to filter contaminants based on protein similarity ?
... Hey guys, I'm familiar with the idea of blob plots, but for filtering off contaminants in a plant I've sequenced. I've so far used a manual screening protocol, whereby I take the top hit of each query ( sim identity , but score and e value) . I then use the uniprot and trembl species identifiers to ...
trembl blastx diamond uniprot written 21 months ago by Biogeek280 • updated 21 months ago by Elisabeth Gasteiger1.5k
0
votes
0
answers
555
views
0
answers
Comment: C: weird e-values with rapsearch
... may i add... the sequences with these values are rather large. i.e +10k bp in size. ...
written 21 months ago by Biogeek280

Latest awards to Biogeek

Popular Question 4 months ago, created a question with more than 1,000 views. For Low number of differentially expressed genes
Popular Question 8 months ago, created a question with more than 1,000 views. For Is There Such A Way/ Program To Do This...
Popular Question 8 months ago, created a question with more than 1,000 views. For Weird Outputs With Dynamictrim And Lengthsort On Custom Settings
Popular Question 8 months ago, created a question with more than 1,000 views. For normalized FPKM matrix file EdgeR and GO Mapping
Great Question 21 months ago, created a question with more than 5,000 views. For MDS plots with R
Epic Question 21 months ago, created a question with more than 10,000 views. For MDS plots with R
Popular Question 21 months ago, created a question with more than 1,000 views. For Can you pool individuals to make 1 biological replicate?
Popular Question 21 months ago, created a question with more than 1,000 views. For MDS plots with R
Popular Question 21 months ago, created a question with more than 1,000 views. For FPKM values / Data analysis
Centurion 23 months ago, created 100 posts.
Scholar 2.3 years ago, created an answer that has been accepted. For A: Visualize groups of conditions bys MDS.
Student 2.3 years ago, asked a question with at least 3 up-votes. For Filtering by FPKM, opinions and thoughts
Great Question 2.4 years ago, created a question with more than 5,000 views. For MDS plots with R
Popular Question 4.1 years ago, created a question with more than 1,000 views. For FPKM values / Data analysis
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Trinity/Rsem/Edger Pipeline...Now What?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For MDS plots with R
Popular Question 4.1 years 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: 1382 users visited in the last hour