Moderator: igor

gravatar for igor
igor12k
Reputation:
11,690
Status:
Trusted
Location:
United States
Last seen:
19 hours ago
Joined:
5 years, 8 months ago
Email:
i********@hotmail.com

Posts by igor

<prev • 1,513 results • page 2 of 152 • next >
0
votes
0
answers
74
views
0
answers
Comment: C: Cell type assignment for non-model organism single cell RNA-seq
... I don't know if it's strange. Even model organisms are manually annotated (many tools exist, but they are usually not sufficient for publication-level analysis). It would be harder to do this for non-model organisms. ...
written 10 days ago by igor12k
1
vote
1
answer
115
views
1
answers
Comment: C: TMM normalized TPM
... No. But you can convert FPKMs to TPMs with a simple formula. See: https://www.biostars.org/p/273370/ ...
written 10 days ago by igor12k
0
votes
0
answers
74
views
0
answers
Comment: C: Cell type assignment for non-model organism single cell RNA-seq
... Do you mean something more advanced than just using a closely related organism? ...
written 10 days ago by igor12k
0
votes
2
answers
150
views
2
answers
Comment: C: Why full-length sequencing is not possible in UMI-based methods in single-cell R
... Doesn't Fluidigm C1 have a UMI option? ...
written 11 days ago by igor12k
4
votes
10
answers
651
views
10
answers
Comment: C: What programming language do you use the most in your work? Which one do you lik
... Most under-appreciated benefit: I can take a perl script from 10 years ago and it will work 95% of the time. Which other mainstream bioinformatic language can you say that about? ...
written 18 days ago by igor12k
0
votes
1
answer
136
views
1
answers
Comment: C: Annotate PBMC scRNA-seq data
... There are multiple discussions on this site about scRNA-seq cell annotation. ...
written 19 days ago by igor12k
0
votes
2
answers
2.5k
views
2
answers
Comment: C: normalization in single cell RNAseq
... In case of 3' datasets, theoretically one transcript results in one count regardless of length, so TPM would be the same as CPM. You would not need to perform additional gene length normalization. Caveat: if you want to account for technical variables like internal priming, things get more complica ...
written 4 weeks ago by igor12k
1
vote
0
answers
207
views
0
answers
Comment: C: Get list of gene signatures published
... It's unfortunate that the main output of the paper is not more clearly described. Curiously, not all of those 613 genes are present in the "OneSubtypeVStheRest" tables. ...
written 4 weeks ago by igor12k
0
votes
0
answers
207
views
0
answers
Comment: C: Get list of gene signatures published
... That sounds reasonable. but what do `sam`, `9`, and `8` refer to? ...
written 4 weeks ago by igor12k
1
vote
1
answer
136
views
1
answers
Answer: A: Annotate PBMC scRNA-seq data
... You can check this tutorial for working with a scATAC and scRNA-seq dataset where they also use PBMC data: https://satijalab.org/signac/articles/pbmc_vignette.html ...
written 4 weeks ago by igor12k

Latest awards to igor

Commentator 18 days ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Great Question 6 weeks ago, created a question with more than 5,000 views. For Faster BLAST alternative
Great Question 6 weeks ago, created a question with more than 5,000 views. For Faster BLAST alternative
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Great Question 7 weeks ago, created a question with more than 5,000 views. For Faster BLAST alternative
Popular Question 9 weeks ago, created a question with more than 1,000 views. For creating visualization tracks for methylation array data
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Scholar 10 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 12 weeks ago, created a question with more than 1,000 views. For creating visualization tracks for methylation array data
Scholar 12 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For Non-computational challenges in bioinformatics
Appreciated 3 months ago, created a post with more than 5 votes. For A: read length of sequence
Appreciated 3 months ago, created a post with more than 5 votes. For A: read length of sequence
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Great Question 4 months ago, created a question with more than 5,000 views. For Faster BLAST alternative
Great Question 5 months ago, created a question with more than 5,000 views. For Faster BLAST alternative
Scholar 7 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Scholar 8 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: defintion of extremely low coverage
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1890 users visited in the last hour
_