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bioconductor-exomepeak
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public |
The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng <[email protected]> if you have any questions.
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2025-04-22 |
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bioconductor-findmyfriends
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public |
Microbial Comparative Genomics in R
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2025-04-22 |
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bioconductor-pathostat
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public |
PathoStat Statistical Microbiome Analysis Package
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2025-04-22 |
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bioconductor-flowmatch
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public |
Matching and meta-clustering in flow cytometry
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2025-04-22 |
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bioconductor-generxcluster
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public |
gRx Differential Clustering
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2025-04-22 |
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bioconductor-batchqc
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public |
Batch Effects Quality Control Software
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2025-04-22 |
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bioconductor-geneselector
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public |
The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.
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2025-04-22 |
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bioconductor-pathrender
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public |
Render molecular pathways
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2025-04-22 |
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bioconductor-pbase
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public |
Manipulating and exploring protein and proteomics data
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2025-04-22 |
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bioconductor-cmap
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public |
Annotation data file for cMAP assembled using data from public data repositories
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2025-04-22 |
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bioconductor-pathvar
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public |
Methods to Find Pathways with Significantly Different Variability
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2025-04-22 |
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bioconductor-genetclassifier
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public |
Classify diseases and build associated gene networks using gene expression profiles
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2025-04-22 |
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bioconductor-minet
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public |
Mutual Information NETworks
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2025-04-22 |
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bioconductor-geneticsdesign
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public |
Functions for designing genetics studies
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2025-04-22 |
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bioconductor-prolocgui
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public |
Interactive visualisation of spatial proteomics data
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2025-04-22 |
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bioconductor-genogam
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public |
A GAM based framework for analysis of ChIP-Seq data
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2025-04-22 |
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bioconductor-pcagopromoter
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public |
pcaGoPromoter is used to analyze DNA micro array data
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2025-04-22 |
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bioconductor-pcpheno
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public |
Phenotypes and cellular organizational units
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2025-04-22 |
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bioconductor-genrank
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public |
Candidate gene prioritization based on convergent evidence
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2025-04-22 |
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bioconductor-quartpac
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public |
Identification of mutational clusters in protein quaternary structures.
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2025-04-22 |
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bioconductor-proloc
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public |
A unifying bioinformatics framework for spatial proteomics
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2025-04-22 |
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bioconductor-geosubmission
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public |
Prepares microarray data for submission to GEO
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2025-04-22 |
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bioconductor-graphpac
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public |
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
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2025-04-22 |
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bioconductor-rarevariantvis
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public |
A suite for analysis of rare genomic variants in whole genome sequencing data
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2025-04-22 |
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bioconductor-spacepac
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public |
Identification of Mutational Clusters in 3D Protein Space via Simulation.
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2025-04-22 |
