User: chrisclarkson100

Reputation:
90
Status:
Trusted
Location:
European Union
Last seen:
1 month ago
Joined:
6 years, 5 months ago
Email:
c***************@yahoo.co.uk

Posts by chrisclarkson100

<prev • 101 results • page 2 of 11 • next >
1
vote
0
answers
1.1k
views
0
answers
Am I correctly converting MotifDb PFMs to PWMs?
... I apologise if some version of this question has already been asked in some way- I could not find any issues that were similar to my own. I have a choice between taking data from the datasource package 'MotifDb' and 'JASPAR2018': MotifDb has a much larger wealth of PFMs: library (MotifDb) ...
pwm sequence pfm written 2.3 years ago by chrisclarkson10090
0
votes
1
answer
1.4k
views
1
answers
Comment: C: trying to reproduce heat map made via cBioportal using download data
... Hi thank you. You're answer is certainly an improvement on mine. ![enter image description here][2] https://ibb.co/giCkcy **As for creating the histogram:** head(data[,c(1:4)]) Hugo_Symbol Entrez_Gene_Id TCGA.3C.AAAU.01 TCGA.3C.AALI.01 1 LOC100130426 100130426 ...
written 2.7 years ago by chrisclarkson10090
0
votes
1
answer
1.4k
views
1
answers
Comment: C: trying to reproduce heat map made via cBioportal using download data
... thanks this has been amended ...
written 2.7 years ago by chrisclarkson10090
0
votes
1
answer
1.4k
views
1
answers
Comment: C: trying to reproduce heat map made via cBioportal using download data
... Hi sorry forgot to add step about "clicking 'Heatmap>>Add genes to heatmap>>cluster heatmap". The question has been modified necessarily. ...
written 2.7 years ago by chrisclarkson10090
2
votes
1
answer
1.4k
views
6 follow
1
answer
trying to reproduce heat map made via cBioportal using download data
... I need to make a statistical comparison using breast cancer data. I have made a heat map at the following link on the Bioportal: http://www.cbioportal.org/index.do?cancer_study_id=brca_tcga&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=brca_tcga_mrna& ...
rna-seq written 2.7 years ago by chrisclarkson10090 • updated 2.7 years ago by Kevin Blighe71k
0
votes
1
answer
939
views
1
answer
differential RNA seq analysis
... I am having trouble selecting a proper GTF file to perform differential RNA-seq analysis (in mm9), using annotation for protein coding genes (or at least all genes, but not pseudogenes). Importantly, I want at the end the quantification of gene expression per gene (not per transcript). Example comma ...
rna-seq written 2.8 years ago by chrisclarkson10090 • updated 2.8 years ago by Friederike6.8k
0
votes
0
answers
1.1k
views
0
answers
can one assess the how well the output of ChromHMM fits the data given to it?
... I have implemented an analysis with ChromHMM, with many histone marks as input. I used a range of different numbers for states and assessed the output of each. for i in {1..10} do java -mx1600M -jar ~/ChromHMM/ChromHMM.jar LearnModel -p 6 ChromHMM_binary ${i}_e $i mm9 done Across a ...
chip-seq chromhmm written 3.3 years ago by chrisclarkson10090
3
votes
3
answers
2.1k
views
3
answers
Answer: A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
... After contacting SRA. It appears that they have done away with the 'SRX' experiment directory: *"The size of the SRA prevents the use of an FTP tree centered around experiments and had to be taken down. If you really need to use the old method of an FTP tree then look at the Runs organized by a stud ...
written 3.3 years ago by chrisclarkson10090
0
votes
3
answers
2.1k
views
3
answers
Comment: C: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
... Thank you for this information but when I try to access the following ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX134/SRX1342333 (also not available). I then search it on the SRA database: SRX1342333 like you did and it is available.... However I just can't seem to access ...
written 3.3 years ago by chrisclarkson10090
9
votes
3
answers
2.1k
views
5 follow
3
answers
SRA has done away with SRX experiment directories on FTP site: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/.... might be temporarily down
... I have been trying all day to access different SRA files on the GEO database but keep being met with '404' kind of error- stating that the site is down. I have tried on two separate computers and get the same result... taking the following path as an example: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sr ...
software error written 3.3 years ago by chrisclarkson10090

Latest awards to chrisclarkson100

Popular Question 9 weeks ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Popular Question 5 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Popular Question 5 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Scholar 6 months ago, created an answer that has been accepted. For A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
Popular Question 9 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Popular Question 9 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 9 months ago, created a question with more than 1,000 views. For Phyre2 vs PSI BLAST comparisons
Popular Question 9 months ago, created a question with more than 1,000 views. For Common match hit between 1st and 2nd round PSI BLAST
Popular Question 9 months ago, created a question with more than 1,000 views. For Jupyter and Anaconda not downloading for me
Popular Question 11 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Popular Question 11 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 11 months ago, created a question with more than 1,000 views. For Common match hit between 1st and 2nd round PSI BLAST
Popular Question 11 months ago, created a question with more than 1,000 views. For Jupyter and Anaconda not downloading for me
Popular Question 11 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Great Question 15 months ago, created a question with more than 5,000 views. For blastn linux command specify database
Popular Question 15 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Popular Question 15 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 15 months ago, created a question with more than 1,000 views. For Common match hit between 1st and 2nd round PSI BLAST
Popular Question 15 months ago, created a question with more than 1,000 views. For Jupyter and Anaconda not downloading for me
Popular Question 15 months ago, created a question with more than 1,000 views. For trying to merge two csv lists of genes with biomaRt
Popular Question 17 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 20 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Centurion 21 months ago, created 100 posts.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
Popular Question 2.0 years ago, created a question with more than 1,000 views. For blastn linux command specify database

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1688 users visited in the last hour
_