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25

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11

replies

3.7k

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6 follow

meta biostars Guidelines

updated 1 day ago by Ram 43k • written 14.6 years ago by Istvan Albert 100k

3

votes

3

replies

191

views

PC

updated 1 day ago by GenoMax 141k • written 1 day ago by Estevão • 0

0

votes

0

replies

155

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annotation scRNA llm

2 days ago by yxwucq • 0

3 results • Page 1 of 1

Recent Votes

Comment: clustalo - align milions of short seq, memory issue

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

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Recent Replies

Answer: Network Alignment by Scooter ▴ 280

Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…

Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host by ZhangYuanfeng • 0

JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…

Comment: PCA plot (Suggestions Needed) by Aaliya ▴ 10

I have actually used DESeq2 data.

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…

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