User: chrisclarkson100

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Posts by chrisclarkson100

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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 14 days ago by chrisclarkson10050
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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 6 months ago by chrisclarkson10050
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Comment: C: trying to reproduce heat map made via cBioportal using download data
... thanks this has been amended ...
written 6 months ago by chrisclarkson10050
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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 6 months ago by chrisclarkson10050
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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 6 months ago by chrisclarkson10050 • updated 6 months ago by Kevin Blighe33k
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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 7 months ago by chrisclarkson10050 • updated 7 months ago by Friederike2.3k
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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 13 months ago by chrisclarkson10050
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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 13 months ago by chrisclarkson10050
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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 13 months ago by chrisclarkson10050
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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 13 months ago by chrisclarkson10050

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