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Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 28 days ago by 41k • written 10.1 years ago by ★ 7.8k
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 24 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
19
votes
13
replies
7.9k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 28 days ago by • 0 • written 17 months ago by 78k
0
votes
4
replies
449
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
20 days ago by Coremine Medical ▴ 20
0
votes
0
replies
171
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 days ago by rohitsatyam102 ▴ 780
5
votes
0
replies
4.2k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
23 days ago by GenoMax 136k
0
votes
0
replies
245
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
26 days ago by rohitsatyam102 ▴ 780
1
vote
0
replies
592
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 24 days ago by 41k • written 8 months ago by ▴ 10
2
votes
0
replies
938
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 17 days ago by • 0 • written 10 months ago by ★ 1.6k
9 results • Page 1 of 1
Recent Votes
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
Seurat integration of two datasets - GSE126783
about batch correction in scRNA-seq
How to compare two Seurat object (sample) in order to find top markers?
How do I resolve an integration error in Seurat?
The difference between merge and integration with Seurat objects
Analyzing single cell RNA seq with multiple samples and conditions
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Comment: How can I map coordinates between two strains of yeast? by Jimmy ▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by GenoMax 136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by newbee ▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's by GenoMax 136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial by GenoMax 136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis? by AK ★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison by CTLong ▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison by CTLong ▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel by MohammadAlkadi ▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data by Kevin Blighe 86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data by Kevin Blighe 86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down by ATpoint 78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down by Katie • 0
I would also appreciate the PDFs if anyone has them please
Answer: Loftee no splice site annotations by AMARU • 0
Hey, did you solve it? I am having a very similar issue. Thanks
Answer: Bulk and Single Cell RNA-seq online course by swbarnes2 13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
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