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bioconductor-glimma
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public |
Interactive visualizations for gene expression analysis
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2025-04-22 |
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bioconductor-keggdzpathwaysgeo
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public |
KEGG Disease Datasets from GEO
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2025-04-22 |
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bioconductor-scpipe
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public |
Pipeline for single cell multi-omic data pre-processing
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2025-04-22 |
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bioconductor-snpchip
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public |
Visualizations for copy number alterations
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2025-04-22 |
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bioconductor-lumi
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public |
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
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2025-04-22 |
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bioconductor-altcdfenvs
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public |
alternative CDF environments (aka probeset mappings)
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2025-04-22 |
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pfam_scan
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public |
pfam_scan.pl is a Perl script calling HMMER v3 to search a FASTA file against a library of Pfam HMMs.
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2025-04-22 |
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bioconductor-derfinder
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public |
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
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2025-04-22 |
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bioconductor-chimera
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public |
A package for secondary analysis of fusion products
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2025-04-22 |
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tracer
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public |
Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.
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2025-04-22 |
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bioconductor-hypergraph
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public |
A package providing hypergraph data structures
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2025-04-22 |
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strainest
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public |
Abundance estimation of strains
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2025-04-22 |
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bioconductor-genbankr
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public |
Parsing GenBank files into semantically useful objects
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2025-04-22 |
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bioconductor-genomicfiles
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public |
Distributed computing by file or by range
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2025-04-22 |
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r-snpassoc
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public |
This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated.
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2025-04-22 |
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consensusfixer
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public |
Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.
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2025-04-22 |
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r-ggsignif
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public |
Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.
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2025-04-22 |
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r-vcfr
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public |
Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
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2025-04-22 |
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r-pinfsc50
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public |
Genomic data for the plant pathogen "Phytophthora infestans." It includes a variant file ('VCF'), a sequence file ('FASTA') and an annotation file ('GFF'). This package is intended to be used as example data for packages that work with genomic data.
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2025-04-22 |
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sccaller
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public |
Dong X et al. Accurate identification of single-nucleotide variants in whole-genome-amplified single cells. Nat Methods. 2017 May;14(5):491-493. doi: 10.1038/nmeth.4227
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2025-04-22 |
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bioconductor-homo.sapiens
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public |
Contains the Homo.sapiens object to access data from several related annotation packages.
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2025-04-22 |
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r-haplo.stats
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public |
Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
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2025-04-22 |
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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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2025-04-22 |
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bioconductor-cytolib
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public |
C++ infrastructure for representing and interacting with the gated cytometry data
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2025-04-22 |
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lohhla
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public |
A computational tool to evaluate HLA loss using next-generation sequencing data.
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2025-04-22 |
