Tag: GPL
Ubuntu Manpage: bamfillquery – fill query sequences into BAM files
Provided by: biobambam2_2.0.179+ds-1_amd64 NAME bamfillquery – fill query sequences into BAM files SYNOPSIS bamfillquery [options] <in.bam queries.fasta >out.bam DESCRIPTION bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data…
Bioconductor – sSNAPPY (development version)
DOI: 10.18129/B9.bioc.sSNAPPY This is the development version of sSNAPPY; for the stable release version, see sSNAPPY. Single Sample directioNAl Pathway Perturbation analYsis Bioconductor version: Development (3.16) A single sample pathway pertrubation testing methods for RNA-seq data. The method propagate changes in gene expression down gene-set topologies to compute…
[Kernel-packages] [Bug 1969434] Autopkgtest regression report (linux-meta-oem-5.17/5.17.0.1005.5)
All autopkgtests for the newly accepted linux-meta-oem-5.17 (5.17.0.1005.5) for jammy have finished running. The following regressions have been reported in tests triggered by the package: dahdi-linux/1:2.11.1~dfsg-1ubuntu11 (amd64) r8168/8.049.02-1ubuntu1 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…
Mbedtls Application On Tcp
How to use mbedTLS library in Keil or IAR IDEs? I want to do an RSA encryption/decryption using my AT91SAM7S256 ARM MCU.After googling I found mbed TLS library. The IP networking interface includes TLSSockets which behave similarly to normal TCP sockets but automatically use Mbed TLS to set up a…
Bioconductor – Rsubread
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…
Bioconductor – neaGUI
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…
Bioconductor – SNPRelate
DOI: 10.18129/B9.bioc.SNPRelate This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SNPRelate. Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data Bioconductor version: 3.12 Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and…
LAMMPS Patch Release 24 March 2022
LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…
licensing – Properly License R Package that Depends on Package from Bioconductor that Imposes Restrictions
I have a problem choosing the right license for my package. My package flowdex depends on some packages from Bioconductor, among them flowWorkspace. flowWorkspace has a file license that says, in short, “academic research only and non-commercial“. Now the question is what license to use in my package flowdex? If…
Bioconductor – cytoKernel
DOI: 10.18129/B9.bioc.cytoKernel Differential expression using kernel-based score test Bioconductor version: Release (3.14) cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression…
Bioconductor – sccomp (development version)
DOI: 10.18129/B9.bioc.sccomp This is the development version of sccomp; to use it, please install the devel version of Bioconductor. Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data Bioconductor version: Development (3.15) A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model…
Bioconductor – GeuvadisTranscriptExpr
DOI: 10.18129/B9.bioc.GeuvadisTranscriptExpr This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see GeuvadisTranscriptExpr. Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project Bioconductor version: 3.8 Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from…
CP2K – Universitetet i Oslo
CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. Description CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional…
Bioconductor – adaptest
DOI: 10.18129/B9.bioc.adaptest This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see adaptest. Data-Adaptive Statistics for High-Dimensional Multiple Testing Bioconductor version: 3.11 Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when…
Bioconductor – txcutr (development version)
DOI: 10.18129/B9.bioc.txcutr This is the development version of txcutr; for the stable release version, see txcutr. Transcriptome CUTteR Bioconductor version: Development (3.15) Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can…
Bioconductor – r3Cseq
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see r3Cseq. Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) Bioconductor version: 3.3 This package is an implementation of data analysis for the long-range interactions from 3C-seq assay. Author: Supat Thongjuea, MRC Molecular…
Bioconductor – pRolocGUI
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see pRolocGUI. Interactive visualisation of spatial proteomics data Bioconductor version: 3.4 The package pRolocGUI comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and shiny. Author: Lisa M…
Bioconductor – DaMiRseq (development version)
DOI: 10.18129/B9.bioc.DaMiRseq This is the development version of DaMiRseq; for the stable release version, see DaMiRseq. Data Mining for RNA-seq data: normalization, feature selection and classification Bioconductor version: Development (3.15) The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them…
Bioconductor – STATegRa (development version)
DOI: 10.18129/B9.bioc.STATegRa This is the development version of STATegRa; for the stable release version, see STATegRa. Classes and methods for multi-omics data integration Bioconductor version: Development (3.15) Classes and tools for multi-omics data integration. Author: STATegra Consortia Maintainer: David Gomez-Cabrero <david.gomezcabrero at ki.se>, Núria Planell <nuria.planell.picola at navarra.es>…
Bioconductor – RDAVIDWebService
DOI: 10.18129/B9.bioc.RDAVIDWebService This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RDAVIDWebService. An R Package for retrieving data from DAVID into R objects using Web Services API. Bioconductor version: 3.12 Tools for retrieving data from the Database for Annotation, Visualization and Integrated…
Bioconductor – bnem (development version)
DOI: 10.18129/B9.bioc.bnem This is the development version of bnem; for the stable release version, see bnem. Training of logical models from indirect measurements of perturbation experiments Bioconductor version: Development (3.15) bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of…
Bioconductor – ChIPQC
This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…
About QUAST
About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…
Bioconductor – monaLisa
DOI: 10.18129/B9.bioc.monaLisa Binned Motif Enrichment Analysis and Visualization Bioconductor version: Release (3.14) Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility…
Bioconductor – ProteoDisco
DOI: 10.18129/B9.bioc.ProteoDisco Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…
Can you use scikit multilearn with scikit-learn?
You can use scikit-learn’s base classifiers as scikit-multilearn’s classifiers. In addition, the two packages follow a similar API. In most cases you will want to follow the requirements defined in the requirements/*.txt files in the package. This will install the latest release from the Python package index. If you Next,…
Bioconductor – Rariant
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see Rariant. Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies Bioconductor version: 3.0 The ‘Rariant’ package identifies single nucleotide variants from sequencing data based on the difference of…
CRAN – Package ggmatplot
CRAN – Package ggmatplot ggmatplot: Plot Columns of Two Matrices Against Each Other Using ‘ggplot2’ A quick and easy way of plotting the columns of two matrices or data frames against each other using ‘ggplot2’. Although ‘ggmatplot’ doesn’t provide the same flexibility as ‘ggplot2’, it can be used as a…
Bioconductor – csaw
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see csaw. ChIP-seq analysis with windows Bioconductor version: 3.2 Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. Author: Aaron Lun <alun at wehi.edu.au>,…
Bioconductor – pageRank
DOI: 10.18129/B9.bioc.pageRank This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see pageRank. Temporal and Multiplex PageRank for Gene Regulatory Network Analysis Bioconductor version: 3.12 Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et…
Bioconductor – CAMERA
DOI: 10.18129/B9.bioc.CAMERA This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see CAMERA. Collection of annotation related methods for mass spectrometry data Bioconductor version: 3.12 Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based…
[v2,01/12] iio:dac:ad5755: Switch to generic firmware properties and drop pdata
@@ -13,10 +13,9 @@ #include <linux/slab.h> #include <linux/sysfs.h> #include <linux/delay.h> -#include <linux/of.h> +#include <linux/property.h> #include <linux/iio/iio.h> #include <linux/iio/sysfs.h> -#include <linux/platform_data/ad5755.h> #define AD5755_NUM_CHANNELS 4 @@ -63,6 +62,101 @@ #define AD5755_SLEW_RATE_SHIFT 3 #define AD5755_SLEW_ENABLE BIT(12) +enum ad5755_mode { + AD5755_MODE_VOLTAGE_0V_5V = 0, + AD5755_MODE_VOLTAGE_0V_10V = 1, + AD5755_MODE_VOLTAGE_PLUSMINUS_5V = 2, + AD5755_MODE_VOLTAGE_PLUSMINUS_10V…
Bioconductor – airpart
DOI: 10.18129/B9.bioc.airpart This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see airpart. Differential cell-type-specific allelic imbalance Bioconductor version: 3.13 Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of…
Bioconductor – TFBSTools
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see TFBSTools. Software Package for Transcription Factor Binding Site (TFBS) Analysis Bioconductor version: 3.3 TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position…
Bioconductor – GenVisR
DOI: 10.18129/B9.bioc.GenVisR Genomic Visualizations in R Bioconductor version: Release (3.5) Produce highly customizable publication quality graphics for genomic data primarily at the cohort level. Author: Zachary Skidmore [aut, cre], Alex Wagner [aut], Robert Lesurf [aut], Katie Campbell [aut], Jason Kunisaki [aut], Obi Griffith [aut], Malachi Griffith [aut] Maintainer:…
Bioconductor – edgeR
DOI: 10.18129/B9.bioc.edgeR Empirical Analysis of Digital Gene Expression Data in R Bioconductor version: Release (3.5) Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood…
Bioconductor – globaltest
Testing groups of covariates/features for association with a response variable, with applications to gene set testing Bioconductor version: 2.5 The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions…
Bioconductor – coGPS
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see coGPS. cancer outlier Gene Profile Sets Bioconductor version: 3.0 Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies Author: Yingying Wei, Michael Ochs Maintainer:…
How can I annotate microarray data set through Ensemble Id?
Hi, I am studying on microarray data set which its platform is the GPL 96([HG-U133A] ). Consequently, I used the GPL 96 annotation file to annotate gene expression data and convert probe ids into gene identifiers. My problem is that in the annotation file I see three columns as gene…
Bioconductor – PathNetData
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see PathNetData. Experimental data for the PathNet package Bioconductor version: 2.13 This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool…
Bioconductor – MmPalateMiRNA
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see MmPalateMiRNA. Murine Palate miRNA Expression Analysis Bioconductor version: 2.13 R package compendium for the analysis of murine palate miRNA two-color expression data. Author: Guy Brock <guy.brock at louisville.edu>, Partha Mukhopadhyay <p0mukh01 at louisville.edu>,…
Bioconductor – SSPA
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see SSPA. General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data Bioconductor version: 3.0 General Sample size and power analysis for microarray and next-generation sequencing data. Author: Maarten van Iterson Maintainer:…
NFP: Network fingerprint analysis in R
This package implements the network fingerprint framework. A biomedical network is characterized as a spectrum-like vector called “network fingerprint”, which contains similarities to basic networks. This knowledge-based multidimensional characterization provides a more intuitive way to decipher molecular networks, especially for large-scale network comparisons and clustering analyses Prerequisites NFP is free…
Bioconductor – svaRetro
DOI: 10.18129/B9.bioc.svaRetro Retrotransposed transcript detection from structural variants Bioconductor version: Release (3.14) svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported…
Bioconductor – cytofast
DOI: 10.18129/B9.bioc.cytofast This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see cytofast. cytofast…
Bioconductor – msPurity
DOI: 10.18129/B9.bioc.msPurity Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics Bioconductor version: Release (3.5) Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called “precursor purity”. Also provides simple processing steps (averaging, filtering, blank subtraction,…
Bioconductor – pRoloc
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see pRoloc. A unifying bioinformatics framework for spatial proteomics Bioconductor version: 3.0 This package implements pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation. Author: Laurent Gatto and Lisa M….
Bioconductor – netresponse
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see netresponse. NetResponse: functional network analysis Bioconductor version: 2.12 Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling. Author: Leo Lahti, Olli-Pekka Huovilainen,…
Bioconductor – dStruct
DOI: 10.18129/B9.bioc.dStruct Identifying differentially reactive regions from RNA structurome profiling data Bioconductor version: Release (3.14) dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al, Genome Biology,…
bioinformatics-ua/DrAC – Giters
DrAC – Drug Annotator for Common data model A solution for extracting Patients’ information from clinical notes and exporting it to an OMOP CDM database. New Features! Annotate medication information in clinical notes Harmonise the resulting information into their standard definition Store extracted drug information into the OMOP CDM Documentation…
Bioconductor – BeadDataPackR
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see BeadDataPackR. Compression of Illumina BeadArray data Bioconductor version: 2.12 Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform Author: Mike Smith, Andy Lynch Maintainer: Mike Smith…
Bioconductor – rBiopaxParser
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see rBiopaxParser. Parses BioPax files and represents them in R Bioconductor version: 3.3 Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported. Author: Frank…
Bioconductor – IntramiRExploreR
DOI: 10.18129/B9.bioc.IntramiRExploreR This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see IntramiRExploreR. Predicting Targets for Drosophila Intragenic miRNAs Bioconductor version: 3.7 Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using…
the standard deviation is zero”
Hi, I am following RnBeads tutorial and with Ziller2011_PLoSGen_450K data set. The tutorial says that the analysis takes 1 1/2 hours on two compute nodes but for me after overnight run with 4 cores it didn’t finish so I had to terminate the process. It seems that there is a…
Bioconductor – cageminer
DOI: 10.18129/B9.bioc.cageminer Candidate Gene Miner Bioconductor version: Release (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally,…
Forcing Rstudio to use a specific version of R on linux
Meta Stack Overflow ,Stack Overflow en español,Stack Overflow em Português, Stack Overflow Public questions & answers load more v I have installed an older R version using the source on a mac, but I am finding it difficult to get Rstudio to see this version. Is there an easy way…
Bioconductor – BgeeCall
DOI: 10.18129/B9.bioc.BgeeCall This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see BgeeCall. Automatic RNA-Seq present/absent gene expression calls generation Bioconductor version: 3.12 BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM Author: Julien Wollbrett [aut, cre],…
Bioconductor – MetaboSignal (development version)
DOI: 10.18129/B9.bioc.MetaboSignal This is the development version of MetaboSignal; for the stable release version, see MetaboSignal. MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways Bioconductor version: Development (3.15) MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG…
Bioconductor – leukemiasEset
DOI: 10.18129/B9.bioc.leukemiasEset This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see leukemiasEset. Leukemia’s microarray gene expression data (expressionSet). Bioconductor version: 3.8 Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia…
Bioconductor – TRESS
DOI: 10.18129/B9.bioc.TRESS Toolbox for mRNA epigenetics sequencing analysis Bioconductor version: Release (3.14) This package is devoted to analyzing MeRIP-seq data. Current functionality is for detection of transcriptome-wide m6A methylation regions. The method is based on hierarchical negative binomial models. Author: Zhenxing Guo [aut, cre], Hao Wu [ctb] Maintainer:…
LAMMPS Patch Release 27 October 2021
LAMMPS Patch Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of interatomic potentials…
Bioconductor – ImpulseDE
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ImpulseDE. Detection of DE genes in time series data using impulse models Bioconductor version: 3.4 ImpulseDE is suited to capture single impulse-like patterns in high throughput time series datasets. By fitting a representative…
How to annotate GPL for GEO data byhand?
How to annotate GPL for GEO data byhand? 1 Hello, getGEO() function always fail to AnnoGPL for GSE69644. Error because 1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption(“download.file.method.GEOquery”)) : cannot open URL ‘https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL13nnn/GPL13667/annot/GPL13667.annot.gz’: HTTP status was ‘404 Not Found’ I want to know how can…
Bioconductor – ADaCGH2
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ADaCGH2. Analysis of data from aCGH experiments using parallel computing and ff objects Bioconductor version: 2.12 Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as…
Bioconductor – BioNet
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see BioNet. Routines for the functional analysis of biological networks Bioconductor version: 3.3 This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can…
Bioconductor – scDataviz
DOI: 10.18129/B9.bioc.scDataviz This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scDataviz. scDataviz: single cell dataviz and downstream analyses Bioconductor version: 3.12 In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need…
Bioconductor – target
DOI: 10.18129/B9.bioc.target This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see target. Predict Combined Function of Transcription Factors Bioconductor version: 3.10 Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) . Extend…
435.gromacs: SPEC CPU2006 Benchmark Description
435.gromacs: SPEC CPU2006 Benchmark Description Benchmark Name 435.gromacs Benchmark Author Erik Lindahl <lindahl [at] gromacs.org>Department of Structural BiologyStockholm Bioinformatics CentreStockholmSweden David van der Spoel <spoel [at] gromacs.org>Department of BiochemistryUppsala UniversityBox 576, 751 23 UppsalaSWEDEN Benchmark Program General Category Chemistry / Molecular Dynamics Benchmark Description 435.gromacs is derived from GROMACS, a…
Bioconductor – esATAC
DOI: 10.18129/B9.bioc.esATAC This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see esATAC. An Easy-to-use Systematic pipeline for ATACseq data analysis Bioconductor version: 3.12 This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw…
interesting kaggle datasets
Kaggle ARC challenge has set May 27 as the final submission deadline for the ARC challenge. Kaggle Datasets. The internet is a treasure trove of valuable information for aspiring data scientists. • updated 2 years ago (Version 3) Data Tasks Code (1,473) Discussion (1) Activity Metadata. (Some might need you…
Bioconductor – rGREAT
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see rGREAT. Client for GREAT Analysis Bioconductor version: 3.2 This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user’s input and automatically retrieving…
Bioconductor – DMRScan
DOI: 10.18129/B9.bioc.DMRScan This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DMRScan. Detection of Differentially Methylated Regions Bioconductor version: 3.10 This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The…
Bioconductor – MADSEQ
DOI: 10.18129/B9.bioc.MADSEQ This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MADSEQ. Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data Bioconductor version: 3.10 The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the…
Bioconductor – Heatplus
DOI: 10.18129/B9.bioc.Heatplus Heatmaps with row and/or column covariates and colored clusters Bioconductor version: Release (3.6) Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is…
Bioconductor – ProteoDisco (development version)
DOI: 10.18129/B9.bioc.ProteoDisco This is the development version of ProteoDisco; to use it, please install the devel version of Bioconductor. Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Development (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions…
Bioconductor – proteinProfiles
DOI: 10.18129/B9.bioc.proteinProfiles Protein Profiling Bioconductor version: Release (3.6) Significance assessment for distance measures of time-course protein profiles Author: Julian Gehring Maintainer: Julian Gehring <jg-bioc at gmx.com> Citation (from within R, enter citation(“proteinProfiles”)): Installation To install this package, start R and enter: ## try http:// if https:// URLs are…
Bioconductor – nethet
DOI: 10.18129/B9.bioc.nethet This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see nethet. A bioconductor package for high-dimensional exploration of biological network heterogeneity Bioconductor version: 3.11 Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional…
Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_
Result for: Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_ Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_ GitHub – rbberger/lammps-doc-utils: Utilities for … Fri, 27 Aug 2021 01:36:00 GMT – This tool is no longer necessary. All of the LAMMPS documentation…
Bioconductor – Melissa
DOI: 10.18129/B9.bioc.Melissa This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Melissa. Bayesian clustering and imputationa of single cell methylomes Bioconductor version: 3.9 Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking…
Bioconductor – PREDA
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see PREDA. Position RElated Data Anlysis Bioconductor version: 3.0 Package for the position related analysis of quantitative functional genomics data. Author: Francesco Ferrari <francesco.ferrari at unimore.it> Maintainer: Francesco Ferrari <francesco.ferrari at unimore.it> Citation (from…
Bioconductor – netprioR
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see netprioR. A model for network-based prioritisation of genes Bioconductor version: 3.4 A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from…
Bioconductor – eisa
This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see eisa. Expression data analysis via the Iterative Signature Algorithm Bioconductor version: 2.9 The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular)…
Bioconductor – rgsepd
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see rgsepd. Gene Set Enrichment / Projection Displays Bioconductor version: 3.4 R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential…
Bioconductor – GeneGA
This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see GeneGA. Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm Bioconductor version: 2.9 R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure…
Bioconductor – Harman
DOI: 10.18129/B9.bioc.Harman This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Harman. The removal of batch effects from datasets using a PCA and constrained optimisation based technique Bioconductor version: 3.12 Harman is a PCA and constrained optimisation based technique that maximises the…
Bioconductor – ERSSA
DOI: 10.18129/B9.bioc.ERSSA This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ERSSA. Empirical RNA-seq Sample Size Analysis Bioconductor version: 3.9 The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate…
Bioconductor – NBAMSeq
DOI: 10.18129/B9.bioc.NBAMSeq This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see NBAMSeq. Negative Binomial Additive Model for RNA-Seq Data Bioconductor version: 3.9 High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step…
Bioconductor – FunciSNP
DOI: 10.18129/B9.bioc.FunciSNP This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FunciSNP. Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Bioconductor version: 3.11 FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in…
Bioconductor – ChIPComp
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…
Bioconductor – MotIV
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MotIV. Motif Identification and Validation Bioconductor version: 3.4 This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize…
Bioconductor – GEOexplorer (development version)
DOI: 10.18129/B9.bioc.GEOexplorer This is the development version of GEOexplorer; to use it, please install the devel version of Bioconductor. GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation Bioconductor version: Development (3.14) GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of…
Bioconductor – GRENITS
This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GRENITS. Gene Regulatory Network Inference Using Time Series Bioconductor version: 2.14 The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear…
Bioconductor – Clomial
DOI: 10.18129/B9.bioc.Clomial This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Clomial. Infers clonal composition of a tumor Bioconductor version: 3.12 Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained…
Bioconductor – MSGFgui
DOI: 10.18129/B9.bioc.MSGFgui A shiny GUI for MSGFplus Bioconductor version: Release (3.5) This package makes it possible to perform analyses using the MSGFplus package in a GUI environment. Furthermore it enables the user to investigate the results using interactive plots, summary statistics and filtering. Lastly it exposes the current…
Bioconductor – wateRmelon
DOI: 10.18129/B9.bioc.wateRmelon This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see wateRmelon. Illumina 450 methylation array normalization and metrics Bioconductor version: 3.11 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages. Author: Leonard…
Bioconductor – conclus
DOI: 10.18129/B9.bioc.conclus ScRNA-seq Workflow CONCLUS – From CONsensus CLUSters To A Meaningful CONCLUSion Bioconductor version: Release (3.13) CONCLUS is a tool for robust clustering and positive marker features selection of single-cell RNA-seq (sc-RNA-seq) datasets. It takes advantage of a consensus clustering approach that greatly simplify sc-RNA-seq data analysis…
Bioconductor – FoldGO
DOI: 10.18129/B9.bioc.FoldGO Package for Fold-specific GO Terms Recognition Bioconductor version: Release (3.13) FoldGO is a package designed to annotate gene sets derived from expression experiments and identify fold-change-specific GO terms. Author: Daniil Wiebe <daniil.wiebe at gmail.com> [aut, cre] Maintainer: Daniil Wiebe <daniil.wiebe at gmail.com> Citation (from within R,…
Bioconductor – tRNAdbImport
DOI: 10.18129/B9.bioc.tRNAdbImport Importing from tRNAdb and mitotRNAdb as GRanges objects Bioconductor version: Release (3.13) tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (trna.bioinf.uni-leipzig.de) as GRanges object. Author: Felix G.M. Ernst [aut, cre] Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com> Citation (from within R, enter citation(“tRNAdbImport”)): Installation To…
Bioconductor – geecc
DOI: 10.18129/B9.bioc.geecc This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see geecc. Gene Set Enrichment Analysis Extended to Contingency Cubes Bioconductor version: 3.11 Use log-linear models to perform hypergeometric and chi-squared tests for gene…
Bioconductor – marr
DOI: 10.18129/B9.bioc.marr Maximum rank reproducibility Bioconductor version: Release (3.13) marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample…