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Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by 141k • written 1 day ago by • 0
0
votes
0
replies
154
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Forum: Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation scRNA llm
1 day ago by yxwucq • 0
4
votes
2
replies
274
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Forum: Bioinformatics: Where do I start
Sequencing
updated 8 days ago by 43k • written 8 days ago by ▴ 10
7
votes
7
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1.1k
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Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 9 days ago by ★ 2.5k • written 10 days ago by • 0
1
vote
2
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332
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Forum: VCF bulk handling
bcftools SnpEff WGS VEP VCF
7 days ago by Javier • 0
16
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10
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1.0k
views
6 follow
Forum: F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 26 days ago by 5.3k • written 27 days ago by ★ 2.4k
103
votes
42
replies
31k
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34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 16 days ago by 22k • written 10.4 years ago by ★ 3.6k
12
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14
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2.4k
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8 follow
Forum: Recovering bam files after unknown deletion in the storage
photorec bam sequencing
written 4.9 years ago by ▴ 70
25
votes
11
replies
3.7k
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6 follow
Forum: Site Use Guidelines
meta biostars Guidelines
updated 1 day ago by 43k • written 14.6 years ago by 100k
9 results • Page 1 of 1
Recent Votes
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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Recent Replies
Comment: Why cd-hit-est not work when sequence identity threshold<0.95？ by Dateline • 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq by Kevin Blighe 87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies by Kevin Blighe 87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue by emmanouil.a ▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package by Pierre Lindenbaum 161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation by Lissa Cruz Saavedra • 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file by swbarnes2 14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model by biochugs • 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed) by Jeremy ▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination by DKA ▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed) by Mensur Dlakic ★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model by Mensur Dlakic ★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed) by Jeremy ▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file by GenoMax 141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
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