Moderator: ATpoint

gravatar for ATpoint
ATpoint46k
Reputation:
45,690
Status:
Trusted
Location:
Last seen:
12 minutes ago
Joined:
4 years, 10 months ago
Email:
a*********@gmail.com

Posts by ATpoint

<prev • 6,675 results • page 2 of 668 • next >
2
votes
1
answer
395
views
1
answers
Comment: C: Which normalization method/pipeline is best to generate normalized counts to mak
... Check http://bioconductor.org/books/release/OSCA/normalization.html#normalization-by-deconvolution It is an awesome read for basically everything related to scRNA-seq with regard to the Bioconductor universe. ...
written 2 days ago by ATpoint46k
0
votes
1
answer
395
views
1
answers
Comment: C: Which normalization method/pipeline is best to generate normalized counts to mak
... The vst is for UMI data though, you would need to check whether all platforms have that. I would use the method in `scran` though tbh as it corrects for compositional changes which you almost certainly will have as different single-cell platforms have different ways of capturing and processing the t ...
written 2 days ago by ATpoint46k
0
votes
1
answer
395
views
1
answers
Comment: C: Which normalization method/pipeline is best to generate normalized counts to mak
... I think you will have a hard time trying to tweak the data for your purposes. Single-cell assays can suffer from severe batch effects between experiments. It is possible to integrate assays, with tools such fastMNN, but this usually results in corrected values in PCA space which can then be used to ...
written 2 days ago by ATpoint46k
0
votes
1
answer
48
views
1
answers
Answer: A: how to build matrices for DeSeq 2 from salmon quan.sf files
... Warning: tl:dr will follow but I guess some background information might be appreciated. => Salmon quantifies against a transcriptome, so the `quant.sf` are transcript abundance estimates. One commonly performs analysis with DESeq2 on the gene level though. The reason is that: a) it is more str ...
written 2 days ago by ATpoint46k
0
votes
0
answers
473
views
0
answers
Comment: C: PanCancerAtlas RNA-SeqV2 (RSEM) file contains negative values
... Please use `ADD REPLY`, the answer box is for answers only. That keeps it logically organized. ...
written 2 days ago by ATpoint46k
0
votes
0
answers
75
views
0
answers
Comment: C: How to insert records in a mysql database with click path?
... Hello USER! We believe that this post does not fit the main topic of this site. After your edit the question is non-sense. Please delete it via `moderate` and then `Delete post`. For this reason we have closed your question. This allows us to keep the site focused on the topics that the communit ...
written 3 days ago by ATpoint46k
0
votes
1
answer
65
views
1
answers
Answer: A: rna-seq/DEseq2 analysis - is it a linear combination problem?
... > I thought about doing ~ sample_time + treatment but I am thinking that I might have problem with all treated samples collected later than the control ones and being unable to separate that from the effects of the treatment. What would be the best way to approach this? Yes, you cannot control f ...
written 3 days ago by ATpoint46k
0
votes
1
answer
395
views
1
answers
Comment: C: Which normalization method/pipeline is best to generate normalized counts to mak
... Do the different datasets contain roughly the same celltypes or is this rather a mishmash of experiments? ...
written 3 days ago by ATpoint46k
1
vote
1
answer
79
views
1
answers
Answer: A: Loading a dataset via acession number
... This is RNA-seq, not microarrays which GEOquery assumes, so it is expected that it produces no output. RNA-seq is sequencing data, you therefore will need to download the fastq files, align/quantify to get a matrix of raw counts. For starters maybe this paper: https://peerj.com/preprints/27283/ Pl ...
written 3 days ago by ATpoint46k
1
vote
1
answer
54
views
1
answers
Answer: A: How to change Rstudio language
... https://stackoverflow.com/questions/13575180/how-to-change-language-settings-in-r ...
written 3 days ago by ATpoint46k

Latest awards to ATpoint

Teacher 6 hours ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 6 hours ago, created an answer that has been accepted. For A: What is the best way to update a list of deprecated gene symbols? (GeCKO v2 gRNA
Teacher 7 hours ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Good Answer 6 days ago, created an answer that was upvoted at least 5 times. For A: Get sequence by genomic coordinates in R
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: Get sequence by genomic coordinates in R
Appreciated 10 days ago, created a post with more than 5 votes. For Salmon Quantification for RNA-seq Read Pairs with Different Lengths
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 11 days ago, created an answer that has been accepted. For A: What is the best way to update a list of deprecated gene symbols? (GeCKO v2 gRNA
Scholar 11 days ago, created an answer that has been accepted. For A: What is the best way to update a list of deprecated gene symbols? (GeCKO v2 gRNA
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Procedure to use Cutadapt toolkit
Teacher 14 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 17 days ago, created an answer that has been accepted. For A: What is the best way to update a list of deprecated gene symbols? (GeCKO v2 gRNA
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 19 days ago, created an answer that has been accepted. For A: What is the best way to update a list of deprecated gene symbols? (GeCKO v2 gRNA
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Popular Question 20 days ago, created a question with more than 1,000 views. For [[ Please read before posting a question ::: How To Ask A Good Question ]]

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2041 users visited in the last hour
_