User: nikitavlassenko

Reputation:
0
Status:
New User
Last seen:
11 hours ago
Joined:
7 months ago
Email:
n**************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by nikitavlassenko

<prev • 21 results • page 1 of 3 • next >
1
vote
0
answers
64
views
0
answers
Sample outlier detection in DESeq2
... I have 16 samples of bulk-RNA-seq data. There are 4 groups, so 4 samples are in each group. I want to check for outliers in each of the groups, and also get some characteristic estimate for each sample in each group of how much of an outlier it is. I am using `DESeq2`. There are threads that I found ...
deseq2 rna-seq written 12 hours ago by nikitavlassenko0 • updated 11 hours ago by genomax46k
0
votes
0
answers
89
views
0
answers
Comment: C: API for cells gene expression levels
... Yeah, ok, I mean gene symbols. Will see then. I just do not need anything (ensembl id, entrez id, whatever) but gene symbols. ...
written 6 days ago by nikitavlassenko0
0
votes
0
answers
89
views
0
answers
Comment: C: API for cells gene expression levels
... Ok, I tried out `EBI` and I suppose I can use `TPM` values in my app. However, there are no `mgi_symbols` in the matrix returned, for instance: ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/data/atlas/rnaseq/studies/arrayexpress/E-GEOD-39230/solanum_tuberosum/genes.tpm.htseq2.tsv So, do I need then ...
written 6 days ago by nikitavlassenko0
0
votes
0
answers
89
views
0
answers
Comment: C: API for cells gene expression levels
... Actually no, but I added the link to the `10X` question ...
written 6 days ago by nikitavlassenko0
0
votes
0
answers
89
views
0
answers
Comment: C: API for cells gene expression levels
... Yes, the question was linked, if I am not mistaken, to the one I also asked on `stackexchange`: https://bioinformatics.stackexchange.com/questions/4024/10x-illumina-demultiplexing-sample-sheet-issue/4046#4046 ...
written 6 days ago by nikitavlassenko0
1
vote
0
answers
89
views
0
answers
API for cells gene expression levels
... I am developing an iOS app to show various data about any cell's type (currently immune cells), and need to find somewhere an API that would let me query a genome database to retrieve gene expression values mainly (but further down the road other data too). I know that there is an 'ImmGen' app on 'A ...
genome database ios written 7 days ago by nikitavlassenko0
0
votes
2
answers
172
views
2
answers
Comment: C: bcl2fastq: Could not parse the CSV stream text
... Sure, their sample test works perfect ...
written 14 days ago by nikitavlassenko0
0
votes
2
answers
172
views
2
answers
Comment: C: bcl2fastq: Could not parse the CSV stream text
... I changed it to two read, not working. Removing all the top thing until `[Data]` gives sample sheet formatting error. Everything looks good in sample sheet, so either I need to somehow find what is actually wrong in samplesheet, some kind of a parsing, verifying program that would tell which line is ...
written 14 days ago by nikitavlassenko0
0
votes
2
answers
172
views
2
answers
Comment: C: bcl2fastq: Could not parse the CSV stream text
... No, it should be 26 8 98 I have 3 reads. I do not understand why `_stderr` file is showing that because I am feeding the correct file in it. That seems very weird for me. ...
written 15 days ago by nikitavlassenko0
0
votes
2
answers
172
views
2
answers
Comment: C: bcl2fastq: Could not parse the CSV stream text
... There is no `dos2unix` installed and I tried to use `tr -d '\r' < input > output` and `perl -pi -e 's/\r\n/\n/g' input` from the following thread: https://unix.stackexchange.com/questions/277217/how-to-install-dos2unix-on-linux-without-root-access But the error stays the same. ...
written 15 days ago by nikitavlassenko0

Latest awards to nikitavlassenko

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1750 users visited in the last hour