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bioconductor-ceu1kg
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public |
CEU (N=60) genotypes from 1000 genomes pilot phase I
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2023-06-16 |
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bioconductor-junctionseq
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public |
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
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2023-06-16 |
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bioconductor-maxcontrastprojection
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public |
Perform a maximum contrast projection of 3D images along the z-dimension into 2D
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2023-06-16 |
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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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2023-06-16 |
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bioconductor-rsffreader
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public |
rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers into similar classes as are present for fastq files.
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2023-06-16 |
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bioconductor-alsace
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public |
ALS for the Automatic Chemical Exploration of mixtures
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2023-06-16 |
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bioconductor-ceuhm3
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public |
ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort
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2023-06-16 |
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r-kinship2
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public |
Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.
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2023-06-16 |
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bioconductor-cand
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public |
Perform Chromosomal Ancestry Differences (CAnD) Analyses
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2023-06-16 |
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bioconductor-snpchip
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public |
Visualizations for copy number alterations
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2023-06-16 |
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bioconductor-affycompatible
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public |
Affymetrix GeneChip software compatibility
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2023-06-16 |
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bioconductor-lmgene
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public |
LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
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2023-06-16 |
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bioconductor-sepa
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public |
Given single-cell RNA-seq data and true experiment time of cells or pseudo-time cell ordering, SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.
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2023-06-16 |
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bioconductor-tarseqqc
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public |
TARgeted SEQuencing Experiment Quality Control
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2023-06-16 |
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bioconductor-ripseeker
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public |
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
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2023-06-16 |
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bioconductor-profia
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public |
Preprocessing of FIA-HRMS data
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2023-06-16 |
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bioconductor-nem
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public |
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
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2023-06-16 |
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bioconductor-pkgdeptools
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public |
Package Dependency Tools
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2023-06-16 |
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bioconductor-papi
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public |
Predict metabolic pathway activity based on metabolomics data
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2023-06-16 |
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bioconductor-qrqc
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public |
Quick Read Quality Control
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2023-06-16 |
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bioconductor-cellgrowth
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public |
Fitting cell population growth models
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2023-06-16 |
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bioconductor-rmat
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public |
This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!
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2023-06-16 |
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bioconductor-netreg
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public |
Network-Regularized Regression Models
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2023-06-16 |
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bioconductor-hicrep
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public |
Measuring the reproducibility of Hi-C data
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2023-06-16 |
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bioconductor-mirsynergy
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public |
Mirsynergy
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2023-06-16 |
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bioconductor-netbiov
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public |
A package for visualizing complex biological network
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2023-06-16 |
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r-scrm
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public |
A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.
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2023-06-16 |
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bioconductor-arraytools
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public |
geneChip Analysis Package
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2023-06-16 |
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bioconductor-bgafun
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public |
BGAfun A method to identify specifity determining residues in protein families
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2023-06-16 |
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bioconductor-plw
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public |
Probe level Locally moderated Weighted t-tests.
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2023-06-16 |
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bioconductor-bac
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public |
Bayesian Analysis of Chip-chip experiment
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2023-06-16 |
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bioconductor-affypdnn
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public |
Probe Dependent Nearest Neighbours (PDNN) for the affy package
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2023-06-16 |
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bioconductor-xbseq
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public |
Test for differential expression for RNA-seq data
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2023-06-16 |
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bioconductor-splicegear
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public |
splicegear
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2023-06-16 |
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bioconductor-mdgsa
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public |
Multi Dimensional Gene Set Analysis.
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2023-06-16 |
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bioconductor-sushi
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public |
Tools for visualizing genomics data
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2023-06-16 |
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bioconductor-roleswitch
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public |
Infer miRNA-mRNA interactions using paired expression data from a single sample
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2023-06-16 |
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bioconductor-rgalaxy
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public |
Make an R function available in the Galaxy web platform
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2023-06-16 |
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r-coloc
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public |
Performs the colocalisation tests described in Plagnol et al (2009) <doi:10.1093/biostatistics/kxn039>, Wallace et al (2013) <doi:10.1002/gepi.21765> and Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>.
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2023-06-16 |
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bioconductor-genomegraphs
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public |
Plotting genomic information from Ensembl
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2023-06-16 |
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bioconductor-genominator
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public |
Analyze, manage and store genomic data
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2023-06-16 |
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bioconductor-tssi
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public |
Identify and normalize transcription start sites in high-throughput sequencing data.
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2023-06-16 |
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bioconductor-annotationfuncs
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public |
Annotation translation functions
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2023-06-16 |
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bioconductor-cancermutationanalysis
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public |
Cancer mutation analysis
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2023-06-16 |
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bioconductor-bayespeak
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public |
Bayesian Analysis of ChIP-seq Data
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2023-06-16 |
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bioconductor-tspair
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public |
Top Scoring Pairs for Microarray Classification
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2023-06-16 |
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bioconductor-chimera
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public |
A package for secondary analysis of fusion products
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2023-06-16 |
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bioconductor-qualifier
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public |
Quality Control of Gated Flow Cytometry Experiments
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2023-06-16 |
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bioconductor-rnaseqmap
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public |
rnaSeq secondary analyses
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2023-06-16 |
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bioconductor-flowcl
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public |
Semantic labelling of flow cytometric cell populations
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2023-06-16 |
