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bioconductor-rnaprobr
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public |
An R package for analysis of massive parallel sequencing based RNA structure probing data
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2023-06-16 |
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chipseq-greylist
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public |
Python implementation of GreyListChIP Bioconductor package.
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2023-06-16 |
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compalignp
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public |
Compute fractional "identity" between trusted alignment and test alignment.
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2023-06-16 |
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mimodd
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public |
Tools for Mutation Identification in Model Organism Genomes
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2023-06-16 |
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perl-yaml-libyaml
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public |
Perl YAML Serialization using XS and libyaml
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2023-06-16 |
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perl-net-ftp-recursive
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public |
Recursive FTP Client class
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2023-06-16 |
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fsnviz
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public |
Tool for plotting gene fusion events detected by various tools using Circos.
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2023-06-16 |
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abyss-k128
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public |
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
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2023-06-16 |
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bioconductor-psicquic
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public |
Proteomics Standard Initiative Common QUery InterfaCe
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2023-06-16 |
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bioconductor-polyfit
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public |
Add-on to DESeq to improve p-values and q-values
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2023-06-16 |
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bioconductor-starr
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public |
Simple tiling array analysis of Affymetrix ChIP-chip data
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2023-06-16 |
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bioconductor-metaarray
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public |
Integration of Microarray Data for Meta-analysis
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2023-06-16 |
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valet
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public |
Pipeline for detecting mis-assemblies in metagenomic assemblies
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2023-06-16 |
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nest
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public |
NEST is a simulator for spiking neural network models.
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2023-06-16 |
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fastqmetrics
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public |
Extract metrics from a fastq file, streaming
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2023-06-16 |
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polymutt
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public |
Li B, Chen W, Zhan X, Busonero F, Sanna S, et al. (2012) A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families. PLoS Genet 8(10): e1002944. doi:10.1371/journal.pgen.1002944
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2023-06-16 |
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bioconductor-calib
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public |
Calibration model for estimating absolute expression levels from microarray data
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2023-06-16 |
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bioconductor-simpleaffy
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public |
Very simple high level analysis of Affymetrix data
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2023-06-16 |
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fishtaco
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public |
No Summary
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2023-06-16 |
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bioconductor-rama
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public |
Robust Analysis of MicroArrays
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2023-06-16 |
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bioconductor-ramigo
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public |
R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Deprecated:Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.
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2023-06-16 |
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bioconductor-atlasrdf
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public |
Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set.
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2023-06-16 |
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bioconductor-pcot2
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public |
Principal Coordinates and Hotelling's T-Square method
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2023-06-16 |
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bioconductor-prada
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public |
Data analysis for cell-based functional assays
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2023-06-16 |
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hicup
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public |
A tool for mapping and performing quality control on Hi-C data
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2023-06-16 |
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bioconductor-ogsa
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public |
Outlier Gene Set Analysis
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2023-06-16 |
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bioconductor-vega
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public |
An R package for copy number data segmentation
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2023-06-16 |
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bioconductor-plethy
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public |
R framework for exploration and analysis of respirometry data
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2023-06-16 |
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bioconductor-affyexpress
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public |
Affymetrix Quality Assessment and Analysis Tool
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2023-06-16 |
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bioconductor-nudge
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public |
Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)
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2023-06-16 |
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musicc
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public |
MUSICC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome.
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2023-06-16 |
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bioconductor-triform
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public |
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
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2023-06-16 |
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snpomatic
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public |
SNP-o-matic is a fast, stringent short-read mapping software.
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2023-06-16 |
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lorma
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public |
LoRMA is a tool for correcting sequencing errors in long reads.
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2023-06-16 |
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plant_tribes_gene_family_integrator
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public |
Gene family integrator pipeline
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2023-06-16 |
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r-ic10trainingdata
|
public |
Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package.
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2023-06-16 |
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backspinpy
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public |
backSPIN clustering algorythm
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2023-06-16 |
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plant_tribes_kaks_analysis
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public |
KaKs Analysis pipeline
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2023-06-16 |
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hicbrowser
|
public |
A simple web browser to visualize Hi-C and other genomic tracks (bigwig, bed, interactions).
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2023-06-16 |
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plant_tribes_gene_family_phylogeny_builder
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public |
Gene family phylogeny builder pipeline
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2023-06-16 |
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cwltool
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public |
Common Workflow Language reference implementation
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2023-06-16 |
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mqc
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public |
qualtiy control tool to assess the mapping quality of a ribosome profiling experiment
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2023-06-16 |
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r-pamr
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public |
Some functions for sample classification in microarrays
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2023-06-16 |
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r-precrec
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public |
Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.
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2023-06-16 |
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strudel
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public |
Strudel is a graphical tool for visualizing genetic and physical maps of genomes for comparative purposes.
|
2023-06-16 |
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r-genabel
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public |
A package for genome-wide association analysis between quantitative or binary traits and single-nucleotide polymorphisms (SNPs).
|
2023-06-16 |
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plant_tribes_gene_family_aligner
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public |
Gene family aligner pipeline
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2023-06-16 |
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segway
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public |
a tool for easy pattern discovery and identification in functional genomics data.
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2023-06-16 |
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curlywhirly
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public |
CurlyWhirly is an application for viewing multi-dimensional data, with a particular focus on the outputs of Principle Coordinate Analysis and Principal Components Analysis
|
2023-06-16 |
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misopy
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public |
Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq
|
2023-06-16 |
