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motifscan
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public |
A package for motif discovery and motif enrichment analysis
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2024-12-19 |
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bioconductor-plier
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public |
Implements the Affymetrix PLIER algorithm
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2024-12-19 |
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umi_tools
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public |
Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs).
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2024-12-19 |
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bioconductor-flowviz
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public |
Visualization for flow cytometry
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2024-12-19 |
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bioconductor-anota
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public |
ANalysis Of Translational Activity (ANOTA).
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2024-12-19 |
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devider
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public |
Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
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2024-12-19 |
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r-grain
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public |
Probability propagation in graphical independence networks, also known as Bayesian networks or probabilistic expert systems.
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2024-12-19 |
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r-genomictools
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public |
A loose collection of tools for the analysis of expression and genotype data, currently with the main focus on (e)QTL and MDR analysis.
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2024-12-19 |
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r-pcalg
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public |
Functions for causal structure learning and causal inference using graphical models. The main algorithms for causal structure learning are PC (for observational data without hidden variables), FCI and RFCI (for observational data with hidden variables), and GIES (for a mix of data from observational studies (i.e. observational data) and data from experiments involving interventions (i.e. interventional data) without hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some related functions are implemented. Functions for incorporating background knowledge are provided.
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2024-12-19 |
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bioconductor-frmatools
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public |
Frozen RMA Tools
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2024-12-19 |
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bioconductor-liebermanaidenhic2009
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public |
Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009)
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2024-12-19 |
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bioconductor-eximir
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public |
R functions for the normalization of Exiqon miRNA array data
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2024-12-19 |
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bioconductor-s4arrays
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public |
Foundation of array-like containers in Bioconductor
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2024-12-19 |
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r-isogene
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public |
Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
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2024-12-19 |
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bioconductor-hapfabia
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public |
hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data
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2024-12-19 |
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abyss
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public |
Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler.
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2024-12-19 |
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bioconductor-rtopper
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public |
This package is designed to perform Gene Set Analysis across multiple genomic platforms
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2024-12-19 |
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bamread
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public |
Read bam files quickly into dataframes in Python
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2024-12-19 |
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bioconductor-hyperdraw
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public |
Visualizing Hypergaphs
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2024-12-19 |
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atropos
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public |
trim adapters from high-throughput sequencing reads
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2024-12-19 |
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bioconductor-spikein
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public |
Affymetrix Spike-In Experiment Data
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2024-12-19 |
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bioconductor-makecdfenv
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public |
CDF Environment Maker
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2024-12-19 |
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bioconductor-panp
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public |
Presence-Absence Calls from Negative Strand Matching Probesets
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2024-12-19 |
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bioconductor-cardinal
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public |
A mass spectrometry imaging toolbox for statistical analysis
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2024-12-19 |
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bioconductor-flowtime
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public |
Annotation and analysis of biological dynamical systems using flow cytometry
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2024-12-19 |
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bioconductor-cghregions
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public |
Dimension Reduction for Array CGH Data with Minimal Information Loss.
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2024-12-19 |
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r-hemdag
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public |
a collection of Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs).
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2024-12-19 |
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bioconductor-cormotif
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public |
Correlation Motif Fit
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2024-12-19 |
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dbghaplo
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public |
Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn Graph.
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2024-12-19 |
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bioconductor-metabocoreutils
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public |
Core Utils for Metabolomics Data
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2024-12-19 |
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bioconductor-cytomem
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public |
Marker Enrichment Modeling (MEM)
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2024-12-19 |
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hits
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public |
Utilities for processing high-throughput sequencing experiments.
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2024-12-19 |
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bioconductor-cytodx
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public |
Robust prediction of clinical outcomes using cytometry data without cell gating
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2024-12-19 |
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bioconductor-reactomegsa.data
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public |
Companion data package for the ReactomeGSA package
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2024-12-19 |
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r-cp4p
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public |
Functions to check whether a vector of p-values respects the assumptions of FDR (false discovery rate) control procedures and to compute adjusted p-values.
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2024-12-19 |
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bioconductor-affydata
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public |
Affymetrix Data for Demonstration Purpose
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2024-12-19 |
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r-mutoss
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public |
Designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying 'mutossGUI'.
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2024-12-19 |
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bioconductor-abarray
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public |
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
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2024-12-19 |
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bioconductor-fedup
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public |
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
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2024-12-19 |
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haproh
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public |
Identify runs of homozygosity (hapROH) and contamination (hapCon) in low coverage ancient human DNA data (1240K SNPs) using modern reference panel
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2024-12-19 |
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bioconductor-rain
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public |
Rhythmicity Analysis Incorporating Non-parametric Methods
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2024-12-19 |
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bioconductor-paircompviz
|
public |
Multiple comparison test visualization
|
2024-12-19 |
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bioconductor-dstruct
|
public |
Identifying differentially reactive regions from RNA structurome profiling data
|
2024-12-19 |
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python-bioext
|
public |
A few handy bioinformatics tools not already in BioPython
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2024-12-19 |
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bioconductor-biocviews
|
public |
Categorized views of R package repositories
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2024-12-19 |
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bioconductor-a4classif
|
public |
Automated Affymetrix Array Analysis Classification Package
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2024-12-19 |
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bioconductor-stategra
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public |
Classes and methods for multi-omics data integration
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2024-12-19 |
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bioconductor-aracne.networks
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public |
ARACNe-inferred gene networks from TCGA tumor datasets
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2024-12-19 |
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bioconductor-curatedbladderdata
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public |
Bladder Cancer Gene Expression Analysis
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2024-12-19 |
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bioconductor-cghcall
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public |
Calling aberrations for array CGH tumor profiles.
|
2024-12-19 |
