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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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sbpipe
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public |
SBpipe is a collection of pipelines for systems modelling of biological networks. It allows mathematical modellers to automatically repeat the tasks of model simulation and parameter estimation, and extract robustness information from these repeat sequences in a solid and consistent manner, facilitating model development and analysis. SBpipe can run models implemented in COPASI, Python or coded in any other programming language using Python as a wrapper module. Pipelines can run on multicore computers, Sun Grid Engine (SGE), Load Sharing Facility (LSF) clusters, or via Snakemake.
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2023-06-16 |
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fgmp
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public |
FGMP: assessing fungal genome completeness and gene content.
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2023-06-16 |
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gneiss
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public |
Compositional data analysis tools and visualizations
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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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sompy
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public |
Numpy based SOM Library.
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2023-06-16 |
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perl-number-range
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public |
Perl extension defining ranges of numbers and testing if a number is found in the range
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2023-06-16 |
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pydemult
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public |
Streamed and parallel demultiplexing of fastq files in python
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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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hulk
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public |
Histosketching Using Little Kmers
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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-phenodist
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public |
PhenoDist is designed for measuring phenotypic distance in image-based high-throughput screening, in order to identify strong phenotypes and to group treatments into functional clusters.
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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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bioconductor-mqtl.nmr
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public |
mQTL.NMR provides a complete mQTL analysis pipeline for 1H NMR data. Distinctive features include normalisation using most-used approaches, peak alignment using RSPA approach, dimensionality reduction using SRV and binning approaches, and mQTL analysis for animal and human cohorts.
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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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vcf-annotator
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public |
Use the reference GenBank file to add biological annotations to the variant calls in a VCF.
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2023-06-16 |
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hotspot3d
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public |
This 3D proximity tool can be used to identify mutation hotspots from linear protein sequence and correlate the hotspots with known or potentially interacting domains, mutations, or drugs. Mutation-mutation and mutation-drug clusters can also be identified and viewed.
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2023-06-16 |
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clust
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public |
Optimised consensus clustering of multiple heterogeneous datasets.
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2023-06-16 |
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kipoiseq
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public |
kipoiseq: sequence-based data-laoders for Kipoi
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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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biopet-bamstats
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public |
BamStats is a package that contains tools to generate stats from a BAM file, merge those stats for multiple samples, and validate the generated stats 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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biopet-scatterregions
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public |
This tool breaks a reference or bed file into smaller scatter regions of equal size.
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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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ctat-mutations
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public |
Mutation detection in RNA-Seq using GATK-v4.0 in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT.
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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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assembly-scan
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public |
Assembly summary statistics in JSON format
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2023-06-16 |
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evofold2
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public |
Identifies functional RNA-structure in multiple sequence alignments.
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2023-06-16 |
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translate-gard
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public |
Converts HyPhy 2.3.2 GARD output to JSON
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2023-06-16 |
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connectome-workbench
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public |
Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project
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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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tiptoft
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public |
Predict plasmids from uncorrected long read data.
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2023-06-16 |
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fred2
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public |
Python-based framework for computational immunomics.
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2023-06-16 |
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slicedimage
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public |
Python module to access sliced imaging data
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2023-06-16 |
