Biostar Forum

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software

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books education

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subjective

updated 12 months ago by Kevin Blighe 86k • written 13.6 years ago by Giovanni M Dall'Olio 28k

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RNA-Seq sequencing papers

updated 14 months ago by Ram 40k • written 7.7 years ago by CandiceChuDVM ★ 2.4k

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scripting

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cheat sheet

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Workshop Training Courses

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project-management file-management

updated 6 months ago by Ram 40k • written 13.4 years ago by Pierre Lindenbaum 157k

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Analyst Scientist

updated 5 months ago by Ram 40k • written 7.4 years ago by Shicheng Guo ★ 9.3k

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r statistics python biopython

updated 7 months ago by Ram 40k • written 10.4 years ago by Medhat 9.7k

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genomics cram gatk galaxy

updated 7 months ago by Ram 40k • written 8.9 years ago by William ★ 5.2k

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updated 11 weeks ago by Ram 40k • written 11.7 years ago by Maxime Lamontagne ★ 2.3k

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updated 5 months ago by zx8754 11k • written 10.5 years ago by Istvan Albert 98k

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updated 10 months ago by Ram 40k • written 10.2 years ago by Medhat 9.7k

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bioinformatics

updated 7 months ago by Ram 40k • written 10.7 years ago by Martin A Hansen 3.0k

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biostars

updated 7 months ago by Ram 40k • written 10.5 years ago by Istvan Albert 98k

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10k

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meta biostars

updated 7 months ago by Ram 40k • written 12.6 years ago by Joachim ★ 2.9k

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Popular Question to ahadli.farid ▴ 50

Recent Replies

Comment: Troubles launch IGV on Linux(Debian) by morovatunc ▴ 550

Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…

Comment: How to check RNAseq support for annotated genes? by Michael 53k

> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…

Comment: Low Alignment rate by Mehwish • 0

Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …

Comment: Violin plot (Monocle 3) - Troubleshooting by Ram 40k

The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…

Comment: Violin plot (Monocle 3) - Troubleshooting by bk11 ★ 1.2k

I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…

Comment: Violin plot (Monocle 3) - Troubleshooting by Ram 40k

What is the output to: ```r help.search('plot_genes_violin', agrep=FALSE, ignore.case=FALSE, fields=c('name')) lsf.str() sessionInfo() ```

Comment: Violin plot (Monocle 3) - Troubleshooting by seattlescientist_01 • 0

I see the error message but I'm confused on what it's telling me.

Answer: Bacterial Pangenome Analysis by liorglic ★ 1.2k

I am not sure I understand why you think there is a problem with your analysis. It makes perfect sense that different blastp cutoffs produc…

Comment: How to plot proportion of cells in each cluster with scanpy? by bioinfo ▴ 110

Thank you for replying again. The "type" still causes issues but the reply by Radu Tanasa worked.

Comment: How to plot proportion of cells in each cluster with scanpy? by bioinfo ▴ 110

Thank you so much. That worked perfectly and it was much faster than what I was trying.

Answer: How to plot proportion of cells in each cluster with scanpy? by Radu Tanasa ▴ 60

Hi. If I get this right, you simply need to compute the percentage of cells in each cluster at the dataset level? ```py import pandas as p…

Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool? by ATpoint 76k

Why would that be an advantage?

Comment: How to plot proportion of cells in each cluster with scanpy? by bk11 ★ 1.2k

The following code will write percentage in your stacked barplot. cross_tab = pd.crosstab(adata.obs['leiden_0.6'],adata.obs['typ…

Comment: How to check RNAseq support for annotated genes? by BioinfoBee • 0

@juke34 Thanks for the suggestion. I wonder if bedtool coverage or intersect can be used to check the transcript support or coverage for ea…

Comment: How to plot proportion of cells in each cluster with scanpy? by bioinfo ▴ 110

Because that was the code from the link. It is how they specified they had 2 groups of samples but I don't have 2 groups. Sorry for the con…

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