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bioconductor-reb
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public |
Regional Expression Biases
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2023-06-16 |
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bioconductor-scsr
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public |
SiRNA correction for seed mediated off-target effect
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2023-06-16 |
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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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2023-06-16 |
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bioconductor-tofsims
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public |
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
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2023-06-16 |
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bioconductor-scfind
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public |
A search tool for single cell RNA-seq data by gene lists
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2023-06-16 |
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bioconductor-bridge
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public |
Bayesian Robust Inference for Differential Gene Expression
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2023-06-16 |
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bioconductor-rgin
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public |
gin in R
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2023-06-16 |
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bioconductor-inversion
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public |
Inversions in genotype data
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2023-06-16 |
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bioconductor-cnvtools
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public |
A package to test genetic association with CNV data
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2023-06-16 |
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r-tigger
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public |
Infers the V genotype of an individual from immunoglobulin (Ig) repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences. Citations: Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>.
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2023-06-16 |
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r-mvr
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public |
This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data. It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. Key features include: (i) Normalization and/or variance stabilization of the data, (ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow), (iii) Generation of diverse diagnostic plots, (iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
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2023-06-16 |
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r-airr
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public |
Schema definitions and read, write and validation tools for data formatted in accordance with the AIRR Data Representation schemas defined by the AIRR Community <http://docs.airr-community.org>.
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2023-06-16 |
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bioconductor-metavizr
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public |
R Interface to the metaviz web app for interactive metagenomics data analysis and visualization
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2023-06-16 |
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bioconductor-ippd
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public |
Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching
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2023-06-16 |
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r-shazam
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public |
Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
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2023-06-16 |
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bioconductor-pathprint
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public |
Pathway fingerprinting for analysis of gene expression arrays
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2023-06-16 |
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bioconductor-chipxpress
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public |
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
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2023-06-16 |
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bioconductor-rariant
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public |
Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
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2023-06-16 |
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bioconductor-networkbma
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public |
Regression-based network inference using Bayesian Model Averaging
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2023-06-16 |
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bioconductor-impulsede
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public |
Detection of DE genes in time series data using impulse models
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2023-06-16 |
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r-bedr
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public |
Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
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2023-06-16 |
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bioconductor-deds
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public |
Differential Expression via Distance Summary for Microarray Data
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2023-06-16 |
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bioconductor-methyanalysis
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public |
DNA methylation data analysis and visualization
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2023-06-16 |
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r-traminer
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public |
Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
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2023-06-16 |
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bioconductor-swimr
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public |
SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
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2023-06-16 |
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bioconductor-spotsegmentation
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public |
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
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2023-06-16 |
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r-nabor
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public |
An R wrapper for 'libnabo', an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D)
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2023-06-16 |
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r-taxa
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public |
Provides taxonomic classes for groupings of taxonomic names without data, and those with data. Methods provided are "taxonomically aware", in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data.
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2023-06-16 |
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bioconductor-rpsixml
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public |
R interface to PSI-MI 2.5 files
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2023-06-16 |
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bioconductor-abaenrichment
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public |
Gene expression enrichment in human brain regions
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2023-06-16 |
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bioconductor-rnaither
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public |
Statistical analysis of high-throughput RNAi screens
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2023-06-16 |
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bioconductor-cancerinsilico
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public |
An R interface for computational modeling of tumor progression
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2023-06-16 |
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bioconductor-linc
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public |
co-expression of lincRNAs and protein-coding genes
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2023-06-16 |
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bioconductor-m3d
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public |
Identifies differentially methylated regions across testing groups
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2023-06-16 |
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r-poppr
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public |
An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
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2023-06-16 |
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bioconductor-gofunction
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public |
GO-function: deriving biologcially relevant functions from statistically significant functions
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2023-06-16 |
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bioconductor-genoset
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public |
A RangedSummarizedExperiment with methods for copy number analysis
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2023-06-16 |
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bioconductor-dmrcate
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public |
Methylation array and sequencing spatial analysis methods
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2023-06-16 |
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r-sequenza
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public |
Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
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2023-06-16 |
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r-polysat
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public |
A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes.
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2023-06-16 |
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bioconductor-dsimer
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public |
dSimer is an R package which provides computation of nine methods for measuring disease-disease similarity, including a standard cosine similarity measure and eight function-based methods. The disease similarity matrix obtained from these nine methods can be visualized through heatmap and network. Biological data widely used in disease-disease associations study are also provided by dSimer.
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2023-06-16 |
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bioconductor-svaplsseq
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public |
SVAPLSseq-An R package to estimate the hidden factors of unwanted variability and adjust for them to enable a more powerful and accurate differential expression analysis based on RNAseq data
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2023-06-16 |
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bioconductor-ppidata
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public |
A package that contains the bait to prey directed graphs for protein-protein interactions
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2023-06-16 |
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r-gpca
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public |
This package implements guided principal components analysis for the detection of batch effects in high-throughput data.
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2023-06-16 |
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bioconductor-htseqtools
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public |
We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.
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2023-06-16 |
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bioconductor-diffloop
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public |
Identifying differential DNA loops from chromatin topology data
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2023-06-16 |
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bioconductor-findmyfriends
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public |
Microbial Comparative Genomics in R
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2023-06-16 |
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r-pegas
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public |
Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
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2023-06-16 |
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bioconductor-kimod
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public |
A k-tables approach to integrate multiple Omics-Data
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2023-06-16 |
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bioconductor-brainstars
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public |
query gene expression data and plots from BrainStars (B*)
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2023-06-16 |
