Bioinformatics Stack Exchange
Bioinformatics Stack Exchange

Most Popular

more tags
1500 questions
3
votes
2 answers

pvalue calculation of protein-protein network with permutation test

Note: this question has also been asked on Biostars I have performed a network recreation analysis based on the interactions of proteins from String db. I wanted to know if the interactions have significance by reshuffling the proteins with…
user3698773
  • 179
  • 3
3
votes
1 answer

What is the R/Bioconductor preferred way of accessing TCGA data?

It seems there are two packages providing access to TCGA data these days: TCGAbiolinks (older) GenomicDataCommons (newer) Will GenomicDataCommons supersede TCGAbiolinks? Is there anything that I might miss if I decide to use only…
Ramiro Magno
  • 165
  • 1
  • 7
3
votes
1 answer

What is the significance of the effect size on WOMAC scores for TKA?

https://www.medicaljournals.se/jrm/content/html/10.2340/16501977-2210 I understand the difference between statistical significance and effect size, but I am having trouble interpreting the data on Table III in the article linked above. I am…
CharlieCal
  • 39
  • 1
3
votes
3 answers

Extract LINE-1 methylation status from WGBS data

I've been trying to figure out the correct way of extracting methylation status of particular elements from WGBS data, and found several possible approaches, but would like to discuss which one could be the best: using software dedicated to the…
Kraken
  • 405
  • 2
  • 9
3
votes
1 answer

genes with highest RPKM/FPKM for a human RNA-seq experiment?

Which genes/transcripts show up as having the highest RPKM/FPKM on a human RNA-seq experiment? Is it usually the same genes/transcripts? EDIT: mRNAs (e.g. poly-A RNA-seq preps) and not including small RNAs.
719016
  • 2,324
  • 13
  • 19
3
votes
4 answers

True bam file encoding and viewing as text

We all have been using samtools to convert between sam and bam files. SAM is tab-delimited file. My question resides on the ability to visualize bam files as text. Is there any way to visualize any bam file as text in linux? Why not work only…
andresito
  • 385
  • 1
  • 3
  • 9
3
votes
1 answer

How to retrieve InChI key for KEGG compound?

I would like to retrieve the InChI representation for a given KEGG compound but I fail to find a direct solution for this (preferably doing it via bioservices). One could do it via ChEBI like this: from bioservices import * kegg_con =…
Cleb
  • 743
  • 7
  • 18
3
votes
1 answer

Database of copy number alterations in different cancer types

Is there a database of somatic copy number alterations (CNAs) in different cancer types? That is, annotations of which CNAs are more commonly seen in different cancer types.
719016
  • 2,324
  • 13
  • 19
3
votes
1 answer

Greedy Motif Search Using Probability Matrices

In my greedy search with pseudocounts algorithm in my bioinformatics course, I did not follow the pseudocode since I wanted to solve the problem in my own way. Unfortunately, although my answer is correct, the answer we are supposed to give is the…
DrJessop
  • 131
  • 1
  • 3
3
votes
4 answers

How to calculate p-values for fold changes?

I'm currently working with data from a Luminex multiplex assay. In this assay, the concentrations of 17 different analyte proteins were identified in 12 groups in triplicate. One of these 17 groups was used as the control, and the log2 fold changes…
J0HN_TIT0R
  • 541
  • 1
  • 4
  • 7
3
votes
2 answers

Can gene co-expression networks be used to help identify differentially expressed genes?

In my RNAseq dataset of differentiated stem-cell lines, some samples have far fewer significantly differentially expressed genes than others. QC shows that this is because there are way fewer reads for one sample than the others. Can gene…
jaslibra
  • 524
  • 2
  • 9
3
votes
2 answers

Why are some of the gene peptides returned by biomaRt missing an asterisk in the end?

Note: this question has also been asked on BioStars I am getting peptides using biomaRt library in R for the gene 'BRCA1'. 27 different aminoacid sequences are returned, and 12 of those have an asterisk (*) in the end, while 15 do not. What does…
user5054
  • 305
  • 1
  • 8
3
votes
1 answer

IGV faster loading remote bigWig files

I noticed remote bigWig files (http URL) take sometimes about 1 minute to load on IGV. Once they loaded, jumping from one region to another can also take several seconds. My understanding is that bigWig files have an internal index for different…
719016
  • 2,324
  • 13
  • 19
3
votes
2 answers

How do I summarise VCF files?

I have got a number of VCF files that all contain data on one particular variant, with every VCF being created from an individual sample. So there is one entry per file (headers…
Nereus
  • 209
  • 1
  • 5
3
votes
1 answer

Annovar index out of date

I'm trying to use Annovar to annotate some variants with their CADD and FATHMM scores. I've downloaded the latest versions of the software and the databases but when I run it I get an error saying the index is out of date. WARNING: Your index file…
Greg
  • 831
  • 6
  • 12
1 2 3
…
99 100