Tag: bioinformatics

49 Resources for learning Markov chain and hidden Markov models 2010-10-04T08:33:05.990

21 What can we learn about the human brain from artificial neural networks? 2015-06-28T22:41:19.243

18 Can the MIC algorithm for detecting non-linear correlations be explained intuitively ? 2011-12-20T01:38:39.507

17 Continuous generalization of the negative binomial distribution 2017-10-29T22:47:34.977

15 Framing the negative binomial distribution for DNA sequencing 2012-09-21T18:57:05.743

15 training approaches for highly-imbalanced data set 2012-11-06T21:28:43.453

13 Making sense out of statistics theory and applications 2011-02-02T14:26:45.833

13 What are the "hot algorithms" for machine learning? 2011-10-18T21:24:39.543

10 What's the difference between statistics and informatics? 2012-06-02T21:02:58.087

10 Enrichment analysis by gene duplication level 2012-12-20T23:35:06.997

8 Calculating the probability of gene list overlap between an RNA seq and a ChIP-chip data set 2011-09-29T23:09:44.517

8 DNA use in court cases 2012-05-14T08:58:27.833

7 What does a random walk do exactly? 2015-03-23T21:07:24.567

6 Independence in gene set enrichment testing 2017-03-27T12:23:44.090

6 Interpretation of p-value histogram for differential methylation analysis: what can explain prevalence of large p-values? 2017-07-07T19:48:55.477

5 Calculating False Acceptance Rate for a Gaussian Distribution of scores 2010-10-11T17:21:37.217

5 What is the advantage of median polish over the median? 2012-07-09T18:38:09.323

5 Binary classification of DNA motif sequences (bioinformatics) 2013-01-14T08:40:38.990

5 Bioinformatical problem - specific word enrichment in a given sequence 2013-06-07T17:19:54.823

5 How to compare two groups when one only has one data point? 2013-08-19T18:21:06.960

4 How to compare two power law distributions? 2011-11-19T21:50:48.507

4 How to find which variables are most correlated with the first principal component? 2014-09-10T20:33:25.457

4 What is the relationship between differential analysis and hierarchial clustering? 2015-07-02T00:59:08.020

4 Cluster analysis with K-means. How to get the cluster representatives? 2016-12-16T09:42:28.543

4 Why does log-transformation of the RNA-seq data reduce the amount of explained variance in PCA? 2017-12-20T20:45:35.910

3 Efficient Empirical CDF Computation / Storage 2010-11-23T23:02:12.753

3 P-value approximation from an underlying unknown distribution 2012-04-17T22:10:48.923

3 How to do 4-parametric regression for ELISA data in R 2013-06-07T09:45:37.763

3 Assumptions in estimating probabilities from a contingency table 2013-07-01T20:14:30.277

3 "Robust" normalization of features from multiple groups and unknown distributions prior to learning 2014-04-02T12:56:56.687

3 Identify differentially expressed genes across genotypes 2016-06-22T21:53:35.160

3 Why do we need to model RNA-seq data using Poisson, negative binomial, 2016-07-09T21:48:38.913

3 Test to determine if the distribution of a subset of points in a bivariate scatterplot differs from the distribution of remaining points 2016-08-20T22:20:39.107

3 Select best model with lasso 2016-09-06T07:20:57.507

3 Odds ratio MLE calculation: unconditional vs conditional? 2017-07-03T18:15:31.850

2 Analysis of variables of varying numbers 2010-10-07T10:50:24.480

2 Interpretation of 3-way ANOVA 2011-04-14T11:20:00.523

2 Clustering large and sparse datasets 2011-05-06T13:34:49.283

2 Validating a model for a set of DNA sequences 2011-10-25T15:10:04.363

2 Binary classification of DNA sequence motifs 2011-11-26T08:06:46.790

2 Statistical tests for low sample numbers in both indendent groups (n=3 and n=1) 2012-04-10T10:34:55.203

2 Proposal for transition matrix for Metropolis-Hastings phylogenetic inference 2012-05-23T06:47:06.527

2 Why genes are assumed to follow multivariate normal? 2013-12-24T18:10:03.613

2 Correcting for multiple testing on non-independent sliding windows 2014-08-21T10:30:10.557

2 DNA sequence classification 2014-11-26T17:09:16.550

2 Probability of a deleterious mutation, given an observed distribution of mutations 2015-03-17T18:32:03.500

2 Calculating residual DTW distance for a subset of the alignment (Dynamic Time Warping) 2015-05-14T00:29:46.753

2 Position Based statistics in DNA sequence 2015-05-20T16:45:42.660

2 Advanced/Professional online data analysis courses 2015-09-21T09:43:14.150

2 Adaptation of binomial testing: How-to? 2015-10-09T15:32:54.583

2 What statistics should I use to combine multiple rankings? 2015-10-23T16:02:23.863

2 Working with subsets of the original data matrices for machine learning 2016-01-15T16:47:53.500

2 Mutations in known DNA sequence: which test to use? 2016-04-15T07:49:49.307

2 What can be the reason to do feature selection based on variance before doing PCA? 2016-05-10T13:53:27.603

2 Combination of Z-scores and hypergeometric distribution? 2016-05-23T13:28:03.827

2 RNA-Seq data distribution 2016-10-10T01:08:57.467

2 Random forest feature importance vs. feature correlation to PCA eigenvectors 2017-01-10T18:39:47.770

2 Survival analyses: how to relevel contrasts for multiple group comparisons? 2017-03-04T13:11:36.620

2 Interaction analysis 2017-04-10T02:22:30.940

2 Single-cell RNA-seq: deep & few or shallow & many? 2017-12-20T19:32:22.000

2 Does ordering the comparisons by p-value make sense? 2018-01-26T09:48:58.947

1 Demo for bioinformatics 2010-12-29T17:48:41.317

1 Assessing DNA sequencing quality 2011-03-11T15:08:43.463

1 Ordered sampling of uniform variables 2011-09-15T08:32:41.783

1 Problem with Bioconductor/limma on two-color factorial design: Coefficients not estimable 2011-10-19T17:36:48.777

1 HMMs in protein or NA sequence alignments 2011-11-15T20:20:11.110

1 Estimating Diversity of operon types using HMMs across metagenomes: Mann-Whitney? Kruskal-Wallis? or other? 2012-05-31T08:35:49.630

1 How to calculate similarity in gene expression for each gene in two conditions and rank them? 2012-06-15T10:29:52.593

1 How to give entire word a quality score to account for the phred score of each letter? 2012-06-15T23:40:10.320

1 GWAS and Statistical theory - does the likelihood of a detectable main effect decrease with complexity? 2012-06-28T23:36:47.483

1 Interpret Silhouette plot for large microarray dataset 2012-10-07T03:20:41.947

1 Limit of quantile normalization 2013-01-28T06:30:52.030

1 Bootstrapping of RNA-Seq data: normal distribution? 2013-08-31T18:39:28.533

1 Given a matrix, each row with a list of numbers, find the most variable rows with an "interesting" pattern 2013-09-19T16:26:02.057

1 Phylogenetic tree with known historical sequences? 2013-09-30T03:49:51.530

1 What is a nonreductive database? 2014-03-04T16:16:00.163

1 Needing help in order to infer the statistical hypothesis tests performed in an old paper 2014-05-06T14:26:34.900

1 How do I calculate the p-value in a gene enrichment analysis, using parametric and non-parametric methods? 2014-06-17T19:03:32.610

1 How to calculate degrees of freedom for chi squared test 2014-06-18T20:31:09.053

1 Repeated multiple regression for LASSO significance testing 2014-07-17T09:18:35.400

1 Un-smoothing/scaling (help normalizing data) 2014-07-28T18:50:22.537

1 Is there any bioinformatic databases gallery webpage like that of biocViews of bioconductor? 2014-08-27T03:21:41.740

1 binomial test for over-represented kmers in biological sequences - what is the right test? 2014-09-17T00:42:55.883

1 Distribution of large set of fold changes 2014-10-21T22:20:35.873

1 Can Anyone explain the significance of Q-mean value? 2014-12-05T16:29:12.537

1 nested multilevel model for differential expression analysis 2014-12-09T15:00:46.130

1 BayesA, BayesB, etc 2015-02-02T23:29:07.220

1 Meaning of confidence interval refered to standard deviation 2015-02-10T11:24:06.753

1 Why is SVM better for bioinformatics analysis? 2015-06-27T13:19:29.307

1 Feature selection with genetic algorithm in R 2015-06-28T10:53:34.490

1 Comparing mutation frequency between a case and a pool of controls 2015-07-29T21:41:03.993

1 Fisher's exact test in RNA-Seq 2016-03-14T12:40:54.733

1 Enrichment of mutations in particular region of the gene 2016-04-05T19:08:06.097

1 How do I optimize a bioinformatics pipeline for novel data sets? 2016-05-16T19:38:36.473

1 Replicates handling in cross-validation 2016-05-14T13:09:07.527

1 RNA-seq: Controlling FDR in multiple contrasts 2016-06-28T22:40:17.560

1 Categorization of variables based on selection process response 2016-08-10T12:38:16.447

1 Underdispersed count data 2016-08-28T11:10:35.247

1 How to interpret Glimmer scores? 2016-09-02T07:32:20.303