User: Bogdan

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Bogdan1.1k
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Posts by Bogdan

<prev • 306 results • page 1 of 31 • next >
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predicted structure of full-length mRNA/lincRNA
... Dear all, would you please let me know if there is a database with RNA secondary/tertiary structure predictions of transcribed RNAs (mRNAs / lincRNAs), that you would recommend please ? thanks a lot, have a good weekend, bogdan ...
sequence rna structure written 13 days ago by Bogdan1.1k
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Comment: C: scRNA-seq, MONOCLE3, and trajectory reconstruction, and Moran I statistics
... Thank you; we have obtained good results by using pseudo-bulk approaches too. Regarding Monocle3 and differential expression, you could please take a look on : https://cole-trapnell-lab.github.io/monocle3/docs/differential/ (we have used graph_test() function in Monocle3). ...
written 4 weeks ago by Bogdan1.1k
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scRNA-seq, MONOCLE3, and trajectory reconstruction, and Moran I statistics
... Dear all, referring to scRNA-seq analysis and Monocle3 trajectory reconstruction in pseudotime (https://cole-trapnell-lab.github.io/monocle3/) : we have 10 samples, and Monocle3 successfully infer the trajectories, however the number of genes that are Diff Expressed along the pseudotime is huge ...
scrna-seq written 4 weeks ago by Bogdan1.1k
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Answer: A: Network analysis: where to start?
... if you'd like to take a look into : https://github.com/gladstone-institutes/Bioinformatics-Workshops/tree/master/intro-pathway-analysis-visualization https://github.com/gladstone-institutes/Bioinformatics-Workshops/tree/master/intro-pathway-modeling and into more advanced workshops too. ...
written 4 weeks ago by Bogdan1.1k
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Comment: C: GO and C++
... thank you, Mensur. yes, I was thinking in the same way ; i was just wondering about the fresh new trends when people develop and implement new algorithms. ...
written 8 weeks ago by Bogdan1.1k
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GO and C++
... Dear all, i was wondering about your opinions please : are many people in bioinformatics / computational biology community writing in GO language instead of using (for example) C++ ? thank you :) -- bogdan ...
c++ go written 8 weeks ago by Bogdan1.1k • updated 8 weeks ago by Juke344.9k
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Comment: C: scRNA-seq data at different time points
... Thank you. Yes, i have been using Conos, Harmony, Seurat3 pipelines for batch correction (as outlined in Seurat wrappers) : https://github.com/satijalab/seurat-wrappers I have came across Tempora for gene expression time series analysis, although I have not tested yet how it works on our data : h ...
written 4 months ago by Bogdan1.1k
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scRNA-seq data at different time points
... Dear all, please may I ask about your suggestions regarding the package(s) to use for the analysis of scRNA_seq data that has been collected at different time points (1,2,3,4,5) and to infer the disease / developmental trajectories on each cell cluster ? thanks a lot, -- bogdan ...
scrna-seq written 4 months ago by Bogdan1.1k • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: computing resources for scRNA-seq analysis
... just a note to add, the pipeline suggested by the authors : https://satijalab.org/seurat/v3.1/integration.html using a reference-based approach seems to be working well. To quote : "we present an additional modification to the Seurat integration workflow, which we refer to as ‘Reference-based’ ...
written 5 months ago by Bogdan1.1k
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Comment: C: computing resources for scRNA-seq analysis
... thank you for sharing your experience, i remember the step : samples.combined.list.anchors <- FindIntegrationAnchors(object.list = samples.combined.list, dims = 1:20) samples.combined.list.combined <- IntegrateData(anchorset = samples.combined.list.anchors, dims = 1:20) when th ...
written 5 months ago by Bogdan1.1k

Latest awards to Bogdan

Popular Question 10 days ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Student 10 days ago, asked a question with at least 3 up-votes. For single cell RNA-seq pipeline
Popular Question 20 days ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Popular Question 8 weeks ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
Popular Question 8 weeks ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 8 weeks ago, created a question with more than 1,000 views. For mutation detection in tumors samples
Popular Question 8 weeks ago, created a question with more than 1,000 views. For linking GATK to MUTECT
Popular Question 8 weeks ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Single Cell RNA Seq. Analysis
Popular Question 4 months ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
Popular Question 4 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 4 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Popular Question 7 months ago, created a question with more than 1,000 views. For SAM file and RNA-seq stranded/unstranded paired/unpaired
Popular Question 7 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 7 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Guru 7 months ago, received more than 100 upvotes.
Student 7 months ago, asked a question with at least 3 up-votes. For filtering the somatic variants
Popular Question 8 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Scholar 8 months ago, created an answer that has been accepted. For A: Calculating fold change at enhancers and promoters
Popular Question 9 months ago, created a question with more than 1,000 views. For running GATK or Mutect or a somatic variant caller individual chromosomes
Popular Question 9 months ago, created a question with more than 1,000 views. For CPU/RAM resources for variant calling
Appreciated 10 months ago, created a post with more than 5 votes. For filtering the somatic variants
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Prophet 10 months ago, created a post with more than 20 followers. For pathogenicity predictors of cancer mutations
Popular Question 10 months ago, created a question with more than 1,000 views. For filtering VCF files

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