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Questions tagged [bioinformatics]

The discipline at the crossroads of computing and the biological sciences, which involves organizing, maintaining, and analyzing data from such fields as molecular biology, genetics, and genomics

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1answer
29 views

mutual information for testing set enrichment?

I've created a process that associates members of two sets, specifically codes from the International Classification of Diseases (ICD) hierarchy and the semantically richer Monarch Disease Ontology (...
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14 views

How to perform feature extraction(PseAAC)?

I am working on K-Post Translational Modification of protein. I have gone thorugh a lot of papers. But there is no detailed view of how to extract feature like PseAAC. Any python code /package is ...
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62 views

Test for significant difference of count data between distributions

I have distributions of counts of DNA segment lengths, and I want to check if a distribution has been significantly increased between "treatments" and across populations. Conceptual example: There ...
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18 views

Combining datasets when working with PCA

I'm largely a statistics novice, and I've gotten into a discussion with my lab mate about the application of PCA. Previously I've applied PCA only to a uniform dataset (results from cells all ...
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22 views

Negative binomial-distribution as background-model: How to calculate the p-value?

I would have a question to the statistics of the following paper: Bioinformatics, Volume 28, Issue 23, 1 December 2012, Pages 3013–3020, https://doi.org/10.1093/bioinformatics/bts569 Simple summary: ...
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1answer
16 views

coefficient of variation and genes highly expressed

I am a biologist, with very little knowledges of statistics. I am looking for highly variable genes from a data set. I have calculated the coefficient of variation of the expressed genes of my dataset ...
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12 views

One-hot encoded fixed-size DNA sequence as output, what loss should I use?

Suppose I have some (deep learning) model that predicts $4 \times n$ (where $n$ fixed) matrices supposedly "unnormalized" one-hot encoded DNA sequences of length $n$, and that I know the ground truth ...
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1answer
26 views

Calculating conditional probability from a query protein sequence

We know there are 20 Amino Acids('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'). Now my query sequence is like: KAQTAHIVLEDGTKMKGYSFGHPSSVA of ...
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17 views

What is the probability of regex pattern occurrence in a string of length n?

I have a string of length n, composed of 20 characters of equal probability. What is chance of occurrence of a regular expression pattern, like 'WP[^WFHY]{5}W' by chance? In case you are not familiar ...
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1answer
40 views

Significance of differences between group-differences

Background: We have RNA-seq data (a method to quantify the expression of genes in a cell) from different cell types. These data were normalized using a method called TMM and then log2-transformed ...
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16 views

Calculating UniFrac distance

So I am trying to calculate unifrac distance for my OTU table, which has about 3000 taxa, 300 samples. Now my phylogenetic tree only consider the most important 500 taxa. My questions are: Do I ...
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0answers
122 views

Interpreting snake-like structures in the UMAP visualization of a FASTA data set

I'm looking for some guidance to interpret a UMAP plot. I started with two FASTA files for two different genes. I concatenated everything into a single string of only ACGT. Then I split that ...
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0answers
36 views

Should a statistical test be performed if power is very low?

I performed some partitioning of data set (genes) into two lists, resulting in two enrichment lists. I wanted to compare them with Fisher's test, but from before I know that similarly looking results ...
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1answer
21 views

have many error likelihoods, how to combine to get a confidence or p value?

I'm working in bioinformatics and its been a long time since I dusted on my statistics. Basically I'm working on variant calling which amounts to sequencing a large number of sequence reads and ...
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1answer
42 views

How to measure interaction between variables (mutations)?

I have a large dataset of germline genetic mutations from a population of 1,000 individuals both affected and non-affected. I've already looked into individual mutations that are enriched in the ...
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0answers
14 views

Significance test for Patient Years

Previously, I had a question about CI for Patient-Years (py) and there was a great answer from @TamasFerenci. Now I need to find out the $p$ value for the py of two different groups. I have a table ...
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1answer
50 views

Is this an example of where I shouldn't scale before doing PCA / PLS?

I'm working with NMR spectra (it's a common chemical test). There are various peaks of the signal across a range of ppm values. I'm trying to relate the NMR spectra of various samples to a ...
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0answers
21 views

Finding first statistically significant point of s curve (sigmoid function) where slope decreases?

Apologies if my title is awful. I have very little statistics experience so I'm hoping the title makes sense. Background on what I'm doing: I'm working on a program that calculates the minimum ...
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1answer
39 views

How to interpret the survival analysis results based on summary results?

I have a gene CFAP97 with expression values and clinical information like FollowupDays and patient_vitalstatus. Using the gene expression data first I classified ...
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2answers
86 views

Preprocessing gene expression dataset

Given a gene expression dataset with 99 samples and 10000 features, it is required to find clusters of samples in the dataset. Now taking the features and finding their means and subtracting those ...
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0answers
29 views

Rank non-normally distributed sets of integers: long read sequencing and phase blocks

I have about 20 arrays of empirical integer values, which are each not normally distributed, with long tails. I am looking for a 'sane and sound' metric on how to sort these distributions, "with ...
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1answer
18 views

Fusion gene detection from TCGA or ICGC data

My PhD project involves fusion gene detection from cancer data of TCGA and ICGC portals. I find that the RNAseq files (fastq,bam formats) are mainly closed access, whereas the clinical or expression ...
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24 views

Overdispersed proportion test?

I am comparing proportions in genomic data. In particular, I compare two populations, A and B, and I look at genetic sites. In other words, I have N contingency tables ...
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0answers
21 views

Normalization of LC-MS data

I am working on a metabolomics project. I am very new to the world of metabolomics. I have been provided an LC-MS dataset in which all the injections are done with the same concentration of the ...
2
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1answer
32 views

Risk prediction equation for disease based on concentrations of circulating proteins

I want to derive a risk prediction equation for disease D based on Pa and Pb, where Pa and Pb are concentrations of circulating proteins in the blood. Disease D has two sub types: Da and Db. In Da, ...
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1answer
130 views

Methods for comparing two dissimilarity matrices

I have run cgMLST on E. coli isolates, then i ran the resulting allele labels through the "daisy" function in R with the "gower" setting to generate a dissimilarity matrix. I have subsets of isolates ...
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0answers
27 views

Adjacency matrix of amino-acid residue [closed]

How to get the mathematical representation of the chemical bonds in protein residue or the whole protein? Is it possible to get the connectivity matrix or a pairwise description? The example in the ...
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0answers
64 views

Why don't my GWAS QQPlots look the same?

I am trying to create a QQPlot of 100 log-transformed p values from a GWAS study. The idea is that taking the -log(p) will magnify the smallest p values to make them easier to see. (reference) I was ...
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50 views

Compare frequencies in HUGE number of categories

I have 2 samples, each with many (e.g. 100'000) different categories (colors in urn model), and counts for each category (number of balls of each color - many with few counts, and few with higher ...
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1answer
268 views

Maximal Information Coefficient (MIC) in practical bioinformatics applications

I am interested in Maximal Information Coefficient (MIC) as an alternative to Pearson correlation when looking at gene co-expression from microarray data. I've read some very good posts on this ...
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1answer
73 views

Genomics Stats Problem

I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding. I have identified 728 sequences of interest. 597 of these ...
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1answer
37 views

A question about pca and gene function analysis

I'm new to bioinformatics, and I have a pretty basic question. Let's say I have a bunch of genes {Xi} and I want to know which one has the most significant on some measurable phenotypic trait Y. Now I ...
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0answers
27 views

test on fold change of the mean vs. mean of fold changes [duplicate]

Suppose we have 5 subjects. For each subject, biomarker is measured at t0, t1 and t2. Measured values are skewed. We want to compare the values at t1 and t2. When we have skewed data, usually we do ...
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0answers
9 views

How to find which type of SV occurs most in a gene?

I am interested in a gene. I have data of what types of structural variants occur in this gene for a patient population (n=300). This gene in total has 200 deletions, 150 duplications, 10 inversions ...
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22 views

About standard deviation expansion

Recently, I read an academic paper. There was a formula that I could't understand. SD represents standard deviation, n (n+1) represents the number of samples. Does anyone know how this formula is ...
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1answer
96 views

What does it mean to apply k-means algorithm on transformed distance matrix?

I am reading a very good (recent) publication in clustering: Kiselev et al., 2017, SC3 - consensus clustering of single-cell RNA-Seq data (if you don't have access, see author PDF). The algorithm ...
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1answer
24 views

Background selection in hypergeometric test using diferent cell types

I have to select the background for an hypergeometric test that I have to perform. The problem is as follow: I have a list of genes differentially expressed in cell B between "control vs treatment"....
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2answers
44 views

What kind of Statistic Method for enrichment or overrepresent should I used for a rank ordered vector with Binary status

I have a gene expression data from 1065 different cell lines, let's say "BRAF" gene. BRAF gene expression levels are ordered. Most TP53 mutated cell lines are high BRAF expression (see the figure ...
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1answer
23 views

Pearson's Correlation on high throughput micrroarray data

I am working in bioinformatics. I am using a microarray data of 24000 genes (attribute) and 170 samples. Is it possible to find Pearson's correlation of 24000 attributes?
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1answer
15 views

Antisense Transcript Level

The basic biology says genes on the DNA, get transcribed to mRNA (sense transcription), and the RNA will be translated to proteins. but sometimes, a gene can have transcription from the opposite ...
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0answers
18 views

Modelling different types of responses to a series of drug concentrations

I have been performing dose response experiments on cancer and control patients for cell counts, apoptosis (flow cytometry DAPI-AnnexinV staining), intracellular protein staining on flow cytometry and ...
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1answer
66 views

How to calculate correlation of 2 variables combined

I have data on 2 histone marks that influence chromatin density. I have calculated individual correlation scores using the cor.test() function in R for both. I would like to combine the 2 together to ...
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1answer
30 views

biological fluorescence supervised machine learning [closed]

Some general questions... So it appears with most classification learners one must come up with a series of quantifiable variables to associate with each observation. This might include mean and std ...
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1answer
74 views

Statistical test for determining hot spot in a heat map

I'm analyzing high through proteomic data and have several thousand 5x5 matrices, where in each matrix the rows and columns refer to different biological conditions, and each cell refers to gene ...
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1answer
315 views

HMM depmixS4 using a vector of known states to fit model

I am using the depmixS4 package to fit HMMs to RNAseq count data. My workflow is as follows: Stack reads into a 'stack' vector which looks like this: ...
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0answers
40 views

Batch effects in survival data

I have a problem concerning batch effects in survival data of C.elegans. I read through a few forum posts and a paper but I am still not really getting it. In the experiment the effect of different ...
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0answers
36 views

Selection of differentially expressed genes

I don't have any statistical background. Have some questions. I see in some research papers they select differentially expressed genes based on fold change and p.value. And in some other papers I ...
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0answers
512 views

How to code a model with the adonis function in R (permanova) for a paired/matched design (epidemiology study)

We have a database of 100 children that are grouped in 50 paired/matched groups (of 2 children) based on co-variables such as sex, c-section, and antibiotic treatments. We obtained the gut microbial ...
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0answers
365 views

Kamada Kawai vs Fruchterman Reingold

I am trying to visualize microbial correlation networks. I am using igraph in R. And my goal is to have weighed edges based on the correlation coefficient between the nodes. I don't understand what ...
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1answer
63 views

Can a Random Forest model trained on an NxM feature matrix be used to predict outcomes on a new feature matrix with k overlapping features?

Context: I'm familiar with the basics of Random Forests, and I'm currently implementing a random forest classifier to make predictions on new proteins using sklearn's ...