Bioconductor package
-
Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, it is currently difficult to evaluate their performance due in part to a lack of sensitive assessment metrics.
12p viaristotle 29-01-2022 6 0 Download
-
Alternative splicing is a biological process during gene expression that allows a single gene to code for multiple proteins. However, splicing patterns can be altered in some conditions or diseases. Here, we present BANDITS, a R/Bioconductor package to perform differential splicing, at both gene and transcript level, based on RNA-seq data.
13p viarchimedes 26-01-2022 12 0 Download
-
High-throughput sequencing data are dramatically increasing in volume. Thus, there is urgent need for efficient tools to perform fast and integrative analysis of multiple data types. Enriched heatmap is a specific form of heatmap that visualizes how genomic signals are enriched over specific target regions. It is commonly used and efficient at revealing enrichment patterns especially for high dimensional genomic and epigenomic datasets.
7p vibeauty 23-10-2021 12 0 Download
-
ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers.
13p vibeauty 23-10-2021 6 0 Download
-
Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining.
8p vitzuyu2711 29-09-2021 16 1 Download
-
Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results.
10p viwyoming2711 16-12-2020 14 0 Download
-
Effective quality assessment is an important part of any high-throughput flow cytometry data analysis pipeline, especially when considering the complex designs of the typical flow experiments applied in clinical trials. Technical issues like instrument variation, problematic antibody staining, or reagent lot changes can lead to biases in the extracted cell subpopulation statistics.
15p viwyoming2711 16-12-2020 19 0 Download
-
Circos is a Perl language based software package for visualizing similarities and differences of genome structure and positional relationships between genomic intervals. Running Circos requires extra data processing procedures to prepare plot data files and configure files from datasets, which limits its capability of integrating directly with other software tools such as R.
5p viwyoming2711 16-12-2020 12 1 Download
-
RNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide fexibility and transparency in the adopted methods.
16p viwyoming2711 16-12-2020 8 0 Download
-
Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often encountered problem, especially for gene expression data.
3p vikentucky2711 26-11-2020 12 1 Download
-
In genome-wide studies, over-representation analysis (ORA) against a set of genes is an essential step for biological interpretation. Many gene annotation resources and software platforms for ORA have been proposed.
17p vikentucky2711 26-11-2020 11 1 Download
-
Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analyses of Hi-C data focus on the detection of statistically significant interactions.
11p vikentucky2711 24-11-2020 5 1 Download
-
In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods.
15p vikentucky2711 24-11-2020 8 1 Download
-
One aspect in which RNA sequencing is more valuable than microarray-based methods is the ability to examine the allelic imbalance of the expression of a gene. This process is often a complex task that entails quality control, alignment, and the counting of reads over heterozygous single-nucleotide polymorphisms.
6p vikentucky2711 24-11-2020 13 1 Download
-
Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers.
12p vioklahoma2711 19-11-2020 24 2 Download
-
Peptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental mass spectra with the theoretically digested peptides derived from a reference protein database.
6p vioklahoma2711 19-11-2020 12 1 Download
-
Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques.
17p vioklahoma2711 19-11-2020 4 1 Download
-
Gene set analysis (in a form of functionally related genes or pathways) has become the method of choice for analyzing omics data in general and gene expression data in particular. There are many statistical methods that either summarize gene-level statistics for a gene set or apply a multivariate statistic that accounts for intergene correlations.
12p vioklahoma2711 19-11-2020 19 1 Download
-
The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the discovery of clinically relevant molecular pathways underlying different diseases and conditions.
13p viconnecticut2711 28-10-2020 11 1 Download
-
Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and -positive interactions make this progress even more complicated. Also, lack of a standard PPIN limits us in the comparison studies and results in the incompatible outcomes.
4p vicoachella2711 27-10-2020 11 0 Download