User: Bogdan

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Bogdan950
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Palo Alto, CA, USA
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1 day, 3 hours ago
Joined:
7 years, 7 months ago
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about me

Posts by Bogdan

<prev • 277 results • page 1 of 28 • next >
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permutation and randomization tests
... Dear all, would you please let me know -- is there any package in R / BioC/ python that has implemented permutation/ randomization tests on genomic regions, in the following way : -- assuming that we have a set of 1000 specific genomic regions (i.e. promoters, enhancers, insulators), and a quantit ...
permutation randomization written 1 day ago by Bogdan950
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about the design of guideRNA for CRISPRko/ CRISPRi/ CRISPRa
... Dear all, i would like to ask for a suggestion about **the design of guideRNA for CRISPRko, CRISPRi, or CRISPRa** experiments. we are using **CHOPCHOP https://chopchop.cbu.uib.no/** to design guideRNAs for CRISPRi , CRISPRko, CRISPRa experiments that target **ENHANCER** regions ; would the gui ...
crispr written 17 days ago by Bogdan950
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Comment: C: a question about filtering and integrating data in Seurat3
... yes, will get back with an extended piece of R code .. ...
written 17 days ago by Bogdan950
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a question about filtering and integrating data in Seurat3
... Dear all, I am following the analysis tutorials on Seurat 3 (on data integration and differential expression), https://satijalab.org/seurat/v3.1/integration.html https://satijalab.org/seurat/v3.1/immune_alignment.html and i would have a question about the FILTERING STEP : at which step shall I ...
scrna-seq seurat3 written 17 days ago by Bogdan950
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Comment: C: normalization methods for scRNA-seq and RNA-seq in specific cases of increased g
... thank you, just re-adjusted the discussion flow (i'm still learning about biostars ;). and yes, we could also use the SPIKE IN controls, if our collaborators are willing to re-do the experiments. ...
written 23 days ago by Bogdan950
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Comment: A: normalization methods for scRNA-seq and RNA-seq in specific cases of increased g
... Hi Devon, thank you for your reply. Beside the use of SPIKE-IN CONTROLS (that we could add to the experiments at a later time point), I believe that we could use also a set of **~ 1130 HOUSEKEEPING GENES** from : http://www.housekeeping.unicamp.br/?download to compute the scaling factors ? Is there ...
written 23 days ago by Bogdan950
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Comment: A: normalization methods for scRNA-seq and RNA-seq in specific cases of increased g
... Hi Devon, thank you for your reply. Beside the use of SPIKE-IN CONTROLS (that we could add to the experiments at a later time point), I believe that we could use also a set of **~ 1130 HOUSEKEEPING GENES** from : http://www.housekeeping.unicamp.br/?download to compute the scaling factors ? Is ther ...
written 23 days ago by Bogdan950
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normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
... Dear all, after re-visiting some articles showing that **C-MYC induces global changes in gene expression,** https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505597/pdf/nihms416894.pdf https://www.sciencedaily.com/releases/2012/10/121025121841.htm where they have used **SPIKE-IN controls for NORMALI ...
scrna-seq rna-seq written 24 days ago by Bogdan950
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Comment: C: about bamToBed and the reads that align to multiple genome coordinates
... thank you, I will check in the SAM file that number of the ALIGNED READS .. ...
written 26 days ago by Bogdan950
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about bamToBed and the reads that align to multiple genome coordinates
... Dear all, I'd like to ask you for your suggestion on the following : when we use `samtools view` and `bamtoBed` in **BEDTOOLS** samtools view "${FILE}.SAM" -Sb | bamToBed -i stdin > "${FILE}.bed" how does BEDTOOLS `bamToBed` handle the reads that start at the same position, or the rea ...
bedtools written 26 days ago by Bogdan950 • updated 26 days ago by RamRS25k

Latest awards to Bogdan

Popular Question 10 days ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 10 days ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Appreciated 23 days ago, created a post with more than 5 votes. For filtering the somatic variants
Popular Question 26 days ago, created a question with more than 1,000 views. For filtering VCF files
Prophet 26 days ago, created a post with more than 20 followers. For pathogenicity predictors of cancer mutations
Popular Question 6 weeks ago, created a question with more than 1,000 views. For filtering VCF files
Student 9 weeks ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Student 9 weeks ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 3 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 3 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 4 months ago, created a question with more than 1,000 views. For filtering VCF files
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to analyze RIP-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 6 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 6 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 6 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 6 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 6 months ago, created a question with more than 1,000 views. For filtering VCF files
Voter 7 months ago, voted more than 100 times.
Appreciated 7 months ago, created a post with more than 5 votes. For filtering the somatic variants
Popular Question 7 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 8 months ago, created a question with more than 1,000 views. For filtering VCF files
Popular Question 10 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 10 months ago, created a question with more than 1,000 views. For filtering VCF files
Good Question 10 months ago, asked a question that was upvoted at least 5 times. For annotation of SV (structural variants)

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