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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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2025-04-22 |
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bioconductor-girafe
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public |
Genome Intervals and Read Alignments for Functional Exploration
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2025-04-22 |
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bioconductor-illuminahumanmethylation450kmanifest
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public |
Manifest for Illumina's 450k array data
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2025-04-22 |
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bioconductor-simlr
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public |
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
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2025-04-22 |
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bioconductor-snagee
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public |
Signal-to-Noise applied to Gene Expression Experiments
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2025-04-22 |
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bioconductor-snageedata
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public |
SNAGEE data
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2025-04-22 |
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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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2025-04-22 |
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biodiff
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public |
exact comparison of biological sequences
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2025-04-22 |
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mvp
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public |
detect creation/destruction of sequence motifs as a result of mutations
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2025-04-22 |
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bioconductor-snm
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public |
Supervised Normalization of Microarrays
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2025-04-22 |
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bioconductor-sigfuge
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public |
SigFuge
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2025-04-22 |
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bioconductor-simat
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public |
GC-SIM-MS data processing and alaysis tool
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2025-04-22 |
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r-canopy
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public |
A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's phylogenetic history. The input are variant allele frequencies (VAFs) of somatic single nucleotide alterations (SNAs) along with allele-specific coverage ratios between the tumor and matched normal sample for somatic copy number alterations (CNAs). These quantities can be directly taken from the output of existing software. Canopy provides a general mathematical framework for pooling data across samples and sites to infer the underlying parameters. For SNAs that fall within CNA regions, Canopy infers their temporal ordering and resolves their phase. When there are multiple evolutionary configurations consistent with the data, Canopy outputs all configurations along with their confidence assessment.
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2025-04-22 |
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tinysink
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public |
Synchronise Nanopore reads with a server.
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2025-04-22 |
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ghostx
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public |
GHOSTX is a homology search tool which can detect remote homologues like BLAST and is about 100 times more efficient than BLAST by using suffix arrays. GHOSTX outputs search results in the format similar to BLAST-tabular format.
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2025-04-22 |
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bioconductor-sigar
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public |
Statistics for Integrative Genomics Analyses in R
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2025-04-22 |
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bioconductor-reactomepa
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public |
Reactome Pathway Analysis
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2025-04-22 |
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bioconductor-reactome.db
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public |
A set of annotation maps for reactome
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2025-04-22 |
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nucamino
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public |
A nucleotide to amino acid alignment program optimized for virus gene sequences
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2025-04-22 |
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bioconductor-slgi
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public |
Synthetic Lethal Genetic Interaction
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2025-04-22 |
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bioconductor-scisi
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public |
In Silico Interactome
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2025-04-22 |
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bioconductor-apcomplex
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public |
Estimate protein complex membership using AP-MS protein data
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2025-04-22 |
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bioconductor-org.sc.sgd.db
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public |
Genome wide annotation for Yeast
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2025-04-22 |
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bioconductor-rpsixml
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public |
R interface to PSI-MI 2.5 files
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2025-04-22 |
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bioconductor-cnvgsa
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public |
Gene Set Analysis of (Rare) Copy Number Variants
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2025-04-22 |
