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bioconductor-a4
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public |
Automated Affymetrix Array Analysis Umbrella Package
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2025-01-03 |
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bioconductor-biocfhir
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public |
Illustration of FHIR ingestion and transformation using R
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2025-01-03 |
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bioconductor-affyilm
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public |
Linear Model of background subtraction and the Langmuir isotherm
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2025-01-03 |
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scarap
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public |
A toolkit for prokaryotic comparative genomics
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2025-01-03 |
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biox
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public |
Biological Sequence Compression Tool
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2025-01-03 |
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r-liger
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public |
Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
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2025-01-03 |
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perl-test-file
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public |
test file attributes
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2025-01-03 |
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chromhmm
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public |
ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks.
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2025-01-03 |
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plasann
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public |
A tool for plasmid annotation and visualization
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2025-01-03 |
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samstrip
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public |
Strip SAM files of data not needed for alignment computations.
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2025-01-03 |
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perl-mce
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public |
Many-Core Engine for Perl providing parallel processing capabilities
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2025-01-03 |
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impg
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public |
impg: implicit pangenome graphs
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2025-01-03 |
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bioconductor-opencyto
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public |
Hierarchical Gating Pipeline for flow cytometry data
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2025-01-03 |
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bioconductor-flowworkspace
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public |
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
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2025-01-03 |
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perl-bio-db-hts
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public |
Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
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2025-01-02 |
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bioconductor-ncdfflow
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public |
ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
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2025-01-02 |
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bioconductor-flowclust
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public |
Clustering for Flow Cytometry
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2025-01-02 |
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bioconductor-flowcore
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public |
flowCore: Basic structures for flow cytometry data
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2025-01-02 |
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perl-bio-bigfile
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public |
Low-level interface to BigWig & BigBed files
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2025-01-02 |
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pybedtools
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public |
Wraps BEDTools for use in Python and adds many additional features.
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2025-01-02 |
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r-pathwaytmb
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public |
A systematic bioinformatics tool to develop a new pathway-based gene panel for tumor mutational burden (TMB) assessment (pathway-based tumor mutational burden, PTMB), using somatic mutations files in an efficient manner from either The Cancer Genome Atlas sources or any in-house studies as long as the data is in mutation annotation file (MAF) format. Besides, we develop a multiple machine learning method using the sample's PTMB profiles to identify cancer-specific dysfunction pathways, which can be a biomarker of prognostic and predictive for cancer immunotherapy.
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2025-01-02 |
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pacini_typing
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public |
YAML-based bacterial genotyping application
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2025-01-02 |
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hicberg
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public |
Statistical profiling based tool for contact data (Hi-C, ChIA-PET, Capture-C, etc.) and genomics data reconstruction
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2025-01-02 |
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kalamari
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public |
A curated database of completed assemblies with taxonomy IDs
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2025-01-02 |
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somaticseq
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public |
An ensemble approach to accurately detect somatic mutations.
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2025-01-02 |
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bioconductor-mvoutdata
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public |
affy and illumina raw data for assessing outlier detector performance
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2025-01-02 |
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bindashtree
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public |
bindashtree is a ultra-fast tool to build genome phylogenetic tree via Binwise Densified MinHash and Rapid Neighbor-joining
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2025-01-02 |
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bioconductor-mitoclone2
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public |
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
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2025-01-02 |
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bioconductor-skewr
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public |
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
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2025-01-02 |
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bioconductor-bigmelon
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public |
Illumina methylation array analysis for large experiments
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2025-01-02 |
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bioconductor-meat
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public |
Muscle Epigenetic Age Test
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2025-01-02 |
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r-redeemr
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public |
R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling.
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2025-01-02 |
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bioconductor-cnvfilter
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public |
Identifies false positives of CNV calling tools by using SNV calls
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2025-01-02 |
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bioconductor-cnviz
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public |
Copy Number Visualization
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2025-01-02 |
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bioconductor-rnaagecalc
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public |
A multi-tissue transcriptional age calculator
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2025-01-02 |
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bioconductor-magar
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public |
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
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2025-01-02 |
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bioconductor-ffpeexampledata
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public |
Illumina DASL example microarray data
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2025-01-02 |
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bioconductor-maqcsubset
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public |
Experimental Data Package: MAQCsubset
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2025-01-02 |
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bioconductor-lumihumanidmapping
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public |
This package includes mappings information between different types of Illumina IDs of Illumina Human chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Human chips to RefSeq IDs with mapping qualities information.
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2025-01-02 |
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bioconductor-lumimouseidmapping
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public |
This package includes mappings information between different types of Illumina IDs of Illumina Mouse chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Mouse chips to RefSeq IDs with mapping qualities information.
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2025-01-02 |
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bioconductor-lumiratidmapping
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public |
This package includes mappings information between different types of Illumina IDs of Illumina Rat chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Rat chips to RefSeq IDs with mapping qualities information.
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2025-01-02 |
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bioconductor-deepsnv
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public |
Detection of subclonal SNVs in deep sequencing data.
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2025-01-02 |
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bioconductor-singlemoleculefootprinting
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public |
Analysis tools for Single Molecule Footprinting (SMF) data
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2025-01-02 |
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bioconductor-quasr
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public |
Quantify and Annotate Short Reads in R
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2025-01-02 |
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bioconductor-ffpe
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public |
Quality assessment and control for FFPE microarray expression data
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2025-01-01 |
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bioconductor-lumibarnes
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public |
Barnes Benchmark Illumina Tissues Titration Data
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2025-01-01 |
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bioconductor-icheck
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public |
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
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2025-01-01 |
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bioconductor-arraymvout
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public |
multivariate outlier detection for expression array QA
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2025-01-01 |
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bioconductor-watermelon
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public |
Illumina DNA methylation array normalization and metrics
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2025-01-01 |
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r-scavenge
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public |
SCAVENGE (Single Cell Analysis of Variant Enrichment through Network propagation of GEnomic data) optimizes the inference of functional and genetic associations to specific cells at single-cell resolution.
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2025-01-01 |
