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bioconductor-metagenomefeatures
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public |
Exploration of marker-gene sequence taxonomic annotations
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2023-06-16 |
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seqmap
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public |
SeqMap is a tool for mapping large amount of oligonucleotide to the genome.
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2023-06-16 |
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python-intervaltree
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public |
Faster than intervaltree_bio
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2023-06-16 |
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bioconductor-snplocs.hsapiens.dbsnp.20120608
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public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 137. The source data files used for this package were created by NCBI on June 7-8, 2012, and contain SNPs mapped to reference genome GRCh37.p5. WARNING: Note that the GRCh37.p5 genome is a patched version of GRCh37 but the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct location but this injection will exclude chrM (i.e. nothing will be injected in that sequence). IMPORTANT NOTE: This package is deprecated. Please use a SNPlocs data package based on a more recent dbSNP BUILD instead (e.g. BUILD 144 or BUILD 149). You can call BSgenome::available.SNPs() from R to get the list of available SNPlocs data packages.
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2023-06-16 |
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bioconductor-nbsplice
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public |
Negative Binomial Models to detect Differential Splicing
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2023-06-16 |
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bioconductor-snplocs.hsapiens.dbsnp.20101109
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public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 132. The source data files used for this package were created by NCBI on 9 November 2010 and contain SNPs mapped to reference genome GRCh37. WARNING: Note that the GRCh37 genome is the same as the hg19 genome from UCSC except for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 but this injection will exclude chrM (i.e. nothing will be injected in that sequence).
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2023-06-16 |
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sparcc
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public |
SparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc).
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2023-06-16 |
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bioconductor-charge
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public |
CHARGE: CHromosome Assessment in R from Gene Expression data
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2023-06-16 |
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bioconductor-lvsmirna
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public |
LVS normalization for Agilent miRNA data
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2023-06-16 |
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pysvmlight
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public |
Interface to Thorsten Joachims' SVM-Light
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2023-06-16 |
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bioconductor-dream4
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public |
Synthetic Expression Data for Gene Regulatory Network Inference from the 2009 DREAM4 challenge
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2023-06-16 |
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bioconductor-prot2d
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public |
The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments
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2023-06-16 |
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perl-module-corelist
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public |
what modules shipped with versions of perl
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2023-06-16 |
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bioconductor-snplocs.hsapiens.dbsnp141.grch38
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public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 141. The source data files used for this package were created by NCBI on May 1st, 2014, and contain SNPs mapped to reference genome GRCh38. Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38. IMPORTANT NOTE: This package is deprecated. Please use a SNPlocs data package based on a more recent dbSNP BUILD instead (e.g. BUILD 144 or BUILD 149). You can call BSgenome::available.SNPs() from R to get the list of available SNPlocs data packages.
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2023-06-16 |
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bioconductor-predictionet
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public |
Inference for predictive networks designed for (but not limited to) genomic data
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2023-06-16 |
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xmatchview
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public |
Genome sequence alignment visualization
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2023-06-16 |
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perl-math-utils
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public |
Useful mathematical functions not in Perl
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2023-06-16 |
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bioconductor-splicesites
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public |
Performs splice centered analysis on RNA-seq data.
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2023-06-16 |
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bioconductor-onesense
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public |
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
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2023-06-16 |
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dropletutils-scripts
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public |
CLI scripts for the DropletUtils package
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2023-06-16 |
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bioconductor-wavetiling
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public |
Wavelet-Based Models for Tiling Array Transcriptome Analysis
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2023-06-16 |
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bioconductor-grridge
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public |
Better prediction by use of co-data: Adaptive group-regularized ridge regression
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2023-06-16 |
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snver
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public |
SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data.
It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained.
Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation.
SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data.
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2023-06-16 |
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bioconductor-netbenchmark
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public |
Benchmarking of several gene network inference methods
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2023-06-16 |
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counterr
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public |
Counterr is a light-weight command line tool that computes errors in sequencing data by comparing the reads to a reference genome.
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2023-06-16 |
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bioconductor-samexplorer
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public |
samExploreR package high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
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2023-06-16 |
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bioconductor-logolas
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public |
EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices
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2023-06-16 |
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bioconductor-stan
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public |
The Genomic STate ANnotation Package
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2023-06-16 |
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bioconductor-narrowpeaks
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public |
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
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2023-06-16 |
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bioconductor-cnpbayes
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public |
Bayesian hierarchical mixture models for batch effects and copy number.
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2023-06-16 |
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cromwell-tools
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public |
Utilities for interacting with the Cromwell workflow engine
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2023-06-16 |
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bioconductor-joda
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public |
JODA algorithm for quantifying gene deregulation using knowledge
|
2023-06-16 |
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bioconductor-googlegenomics
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public |
Provides an R package to interact with the Google Genomics API.
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2023-06-16 |
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bioconductor-signet
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public |
signet: Selection Inference in Gene NETworks
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2023-06-16 |
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bioconductor-genphen
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public |
genphen: tool for quantification of genotype-phenotype associations in genome wide association studies (GWAS)
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2023-06-16 |
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bioconductor-methvisual
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public |
Methods for visualization and statistics on DNA methylation data
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2023-06-16 |
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bioconductor-reb
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public |
Regional Expression Biases
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2023-06-16 |
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bioconductor-scsr
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public |
SiRNA correction for seed mediated off-target effect
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2023-06-16 |
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r-seurat-scripts
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public |
A set of wrappers for individual components of the Seurat package. Functions R packages are hard to call when building workflows outside of R, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects, but the ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.
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2023-06-16 |
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bioconductor-geneselector
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public |
The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.
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2023-06-16 |
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bioconductor-tofsims
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public |
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
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2023-06-16 |
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bioconductor-scfind
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public |
A search tool for single cell RNA-seq data by gene lists
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2023-06-16 |
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bioconductor-bridge
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public |
Bayesian Robust Inference for Differential Gene Expression
|
2023-06-16 |
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bioconductor-rgin
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public |
gin in R
|
2023-06-16 |
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bioconductor-inversion
|
public |
Inversions in genotype data
|
2023-06-16 |
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bioconductor-cnvtools
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public |
A package to test genetic association with CNV data
|
2023-06-16 |
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rvtests
|
public |
Rare variant test software for next generation sequencing data
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2023-06-16 |
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r-goeveg
|
public |
A collection of functions useful in (vegetation) community analyses and ordinations, mainly to facilitate plotting and interpretation. Includes automatic species selection for ordination diagrams, species response curves and rank-abundance curves.
|
2023-06-16 |
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var-agg
|
public |
A simple helper for aggregating multi-sample VCF files into "site VCF" files.
|
2023-06-16 |
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pyaavf
|
public |
An amino acid variant format parser for Python.
|
2023-06-16 |
