Tag: GPL

Bioconductor – ChromSCape

DOI: 10.18129/B9.bioc.ChromSCape     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ChromSCape. Analysis of single-cell epigenomics datasets with a Shiny App Bioconductor version: 3.15 ChromSCape – Chromatin landscape profiling for Single Cells – is a ready-to-launch user-friendly Shiny Application for the analysis…

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Bioconductor – MuData

DOI: 10.18129/B9.bioc.MuData     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see MuData. Serialization for MultiAssayExperiment Objects Bioconductor version: 3.15 Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an…

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Bioconductor – topdownr

DOI: 10.18129/B9.bioc.topdownr     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see topdownr. Investigation of Fragmentation Conditions in Top-Down Proteomics Bioconductor version: 3.14 The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to…

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Bioconductor – deco

DOI: 10.18129/B9.bioc.deco     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see deco. Decomposing Heterogeneous Cohorts using Omic Data Profiling Bioconductor version: 3.15 This package discovers differential features in hetero- and homogeneous omic data by a two-step method including subsampling LIMMA and NSCA….

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Bioconductor – OpenStats

DOI: 10.18129/B9.bioc.OpenStats     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see OpenStats. A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association Bioconductor version: 3.12 Package contains several methods for statistical analysis of genotype to phenotype association in high-throughput…

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Sage Math HappyMod video reviews.

Name Sage Math Package Name org.sagemath.droid Publisher: VW4EG566 Category Version 1.0.1 Size 1.85 MB Price FREE Requires Android 2.3 (GINGERBREAD) Android client for the Sage open-source mathematical software system. Please use groups.google.com/group/sage-devel for feedback until the release is finished! GPL source code at github.com/sagemath/android For a good keyboard app to…

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Bioconductor – APL

DOI: 10.18129/B9.bioc.APL     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see APL. Association Plots Bioconductor version: 3.15 APL is a package developed for computation of Association Plots (AP), a method for visualization and analysis of single cell transcriptomics data. The main focus…

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[PATCH v4 1/6] gnu: mbedtls-apache: Rename package to mbedtls-apache-lts.

* gnu/packages/tls.scm (mbedtls-apache): Rename from this… (mbedtls-apache-lts): … to this. (mbedtls-for-hiawatha): Adjust accordingly. * gnu/packages/emulators.scm (dolphin-emu)[inputs]: Adjust inputs accordingly. * gnu/packages/game-development.scm (godot)[inputs]: Likewise. * gnu/packages/hardware.scm (hueplusplus,openrgb)[inputs]: Likewise. * gnu/packages/haxe.scm (neko,haxe,hashlink)[inputs]: Likewise. * gnu/packages/irc.scm (inspircd)[inputs]: Likewise. * gnu/packages/julia-jll.scm (julia-mbedtls-jll)[inputs]: Likewise. * gnu/packages/julia.scm (julia)[inputs]: Likewise. * gnu/packages/linphone.scm (bctoolbox)[inputs]: Likewise. * gnu/packages/linux.scm (dislocker)[inputs]:…

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Bioconductor – cfdnakit (development version)

DOI: 10.18129/B9.bioc.cfdnakit   This is the development version of cfdnakit; to use it, please install the devel version of Bioconductor. Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA) Bioconductor version: Development (3.18) This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA…

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Bioconductor – HiBED (development version)

DOI: 10.18129/B9.bioc.HiBED   This is the development version of HiBED; to use it, please install the devel version of Bioconductor. HiBED Bioconductor version: Development (3.18) Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic…

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Bioconductor – CHARGE

DOI: 10.18129/B9.bioc.CHARGE     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CHARGE. CHARGE: CHromosome Assessment in R from Gene Expression data Bioconductor version: 3.9 Identifies genomic duplications or deletions from gene expression data. Author: Benjamin Mayne Maintainer: Benjamin Mayne <benjamin.mayne at sahmri.com>…

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Bioconductor – iNETgrate (development version)

DOI: 10.18129/B9.bioc.iNETgrate   This is the development version of iNETgrate; to use it, please install the devel version of Bioconductor. Integrates DNA methylation data with gene expression in a single gene network Bioconductor version: Development (3.18) The iNETgrate package provides functions to build a correlation network in which nodes are…

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Bioconductor – adSplit

DOI: 10.18129/B9.bioc.adSplit     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see adSplit. Annotation-Driven Clustering Bioconductor version: 3.13 This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are…

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Bioconductor – BatchQC

DOI: 10.18129/B9.bioc.BatchQC     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see BatchQC. Batch Effects Quality Control Software Bioconductor version: 3.13 Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that…

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Bioconductor – chromPlot

DOI: 10.18129/B9.bioc.chromPlot     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see chromPlot. Global visualization tool of genomic data Bioconductor version: 3.13 Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at…

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Arch Linux – slurm-llnl 22.05.8.1-1 (x86_64)

slurm-llnl 22.05.8.1-1 Architecture: x86_64 Repository: Extra Description: Simple Linux Utility for Resource Management Upstream URL: www.schedmd.com License(s): GPL Maintainers: Felix Yan Package Size: 5.1 MB Installed Size: 17.4 MB Last Packager: Felix Yan Build Date: 2023-03-26 07:12 UTC Signed By: Felix Yan Signature Date: 2023-03-26 07:17 UTC Last Updated: 2023-05-19 17:19 UTC…

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Bioconductor – CNORfeeder

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see CNORfeeder. Integration of CellNOptR to add missing links Bioconductor version: 2.13 This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with…

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Bioconductor – GmicR

DOI: 10.18129/B9.bioc.GmicR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GmicR. Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC) Bioconductor version: 3.13 This package uses bayesian network learning to detect relationships between Gene…

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Bioconductor – iASeq

DOI: 10.18129/B9.bioc.iASeq     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see iASeq. iASeq: integrating multiple sequencing datasets for detecting allele-specific events Bioconductor version: 3.13 It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and…

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Bioconductor – sparsenetgls

DOI: 10.18129/B9.bioc.sparsenetgls     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see sparsenetgls. Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression Bioconductor version: 3.13 The package provides methods of combining the graph structure learning and generalized…

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Bioconductor – tximport

DOI: 10.18129/B9.bioc.tximport     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see tximport. Import and summarize transcript-level estimates for transcript- and gene-level analysis Bioconductor version: 3.13 Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level…

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Bioconductor – Trendy

DOI: 10.18129/B9.bioc.Trendy     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Trendy. Breakpoint analysis of time-course expression data Bioconductor version: 3.13 Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput…

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Bioconductor – peco

DOI: 10.18129/B9.bioc.peco     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see peco. A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data Bioconductor version: 3.13 Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently,…

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Bioconductor – maPredictDSC

DOI: 10.18129/B9.bioc.maPredictDSC     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see maPredictDSC. Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge Bioconductor version: 3.13 This package implements the classification pipeline of the best overall…

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Bioconductor – trackViewer

DOI: 10.18129/B9.bioc.trackViewer   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see trackViewer. A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data Bioconductor version: 3.16 Visualize mapped reads along with annotation as…

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Bioconductor – REMP

DOI: 10.18129/B9.bioc.REMP     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see REMP. Repetitive Element Methylation Prediction Bioconductor version: 3.13 Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide…

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an observational prospective study in chronic pain with sex-differences

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Bioconductor – rpx

DOI: 10.18129/B9.bioc.rpx     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see rpx. R Interface to the ProteomeXchange Repository Bioconductor version: 3.13 The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium. Author: Laurent Gatto Maintainer: Laurent Gatto <laurent.gatto…

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Bioconductor – methylGSA

DOI: 10.18129/B9.bioc.methylGSA     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see methylGSA. Gene Set Analysis Using the Outcome of Differential Methylation Bioconductor version: 3.13 The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as…

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Bioconductor – CompGO

DOI: 10.18129/B9.bioc.CompGO     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 CompGO. An…

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Bioconductor – geneplast

DOI: 10.18129/B9.bioc.geneplast     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see geneplast. Evolutionary and plasticity analysis of orthologous groups Bioconductor version: 3.13 Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses…

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Bioconductor – MatrixQCvis

DOI: 10.18129/B9.bioc.MatrixQCvis     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MatrixQCvis. Shiny-based interactive data-quality exploration for omics data Bioconductor version: 3.13 Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here…

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Bioconductor – RcisTarget

DOI: 10.18129/B9.bioc.RcisTarget     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RcisTarget. RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions Bioconductor version: 3.13 RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list….

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R+ggplot2+facet_wrap: preserve the with of the bars

Please have a look at the reprex at the end of the post. It is a faceted barchart where the bars are placed in decreasing order in each subplot. My only question is how to ensure that the bars have the same consistent width in all the subplots. I had…

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Bioconductor – spkTools

Methods for Spike-in Arrays Bioconductor version: 2.5 The package contains functions that can be used to compare expression measures on different array platforms. Author: Matthew N McCall <mmccall at jhsph.edu>, Rafael A Irizarry <rafa at jhu.edu> Maintainer: Matthew N McCall <mmccall at jhsph.edu> To install this package, start R and…

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[PATCH 1/3] w1: gpio: Don’t use platform data for driver data

[PATCH 1/3] w1: gpio: Don’t use platform data for driver data – Uwe Kleine-König From: “Uwe Kleine-König” <u.kleine-koenig@pengutronix.de> To: Krzysztof Kozlowski <krzysztof.kozlowski@linaro.org> Cc: Rob Herring <robh@kernel.org>, Greg Kroah-Hartman <gregkh@linuxfoundation.org>, linux-kernel@vger.kernel.org, Philipp Marek <philipp@marek.priv.at> Subject: [PATCH 1/3] w1: gpio: Don’t use platform data for driver data Date: Thu, 25 May 2023…

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Bioconductor – phenoTest

DOI: 10.18129/B9.bioc.phenoTest     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see phenoTest. Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis)…

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Arch Linux – sagemath-doc 9.8-1 (any)

sagemath-doc 9.8-1 Architecture: any Repository: Extra Description: HTML documentation for SageMath Upstream URL: www.sagemath.org License(s): GPL Maintainers: Antonio Rojas Package Size: 35.6 MB Installed Size: 430.1 MB Last Packager: Antonio Rojas Build Date: 2023-02-12 10:16 UTC Signed By: Antonio Rojas Signature Date: 2023-02-12 10:49 UTC Last Updated: 2023-05-19 16:42 UTC Read more…

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Arch Linux – sagemath 9.8-4 (x86_64)

sagemath 9.8-4 Architecture: x86_64 Repository: Extra Description: Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab Upstream URL: www.sagemath.org License(s): GPL Replaces: sagemath-jupyter Conflicts: sagemath-jupyter Maintainers: Antonio Rojas Package Size: 53.5 MB Installed Size: 484.3 MB Last Packager: Antonio Rojas Build Date: 2023-05-04 11:51 UTC Signed By: Antonio Rojas…

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Babraham Bioinformatics – FastQC A Quality Control tool for High Throughput Sequence Data

FastQC Function AMPERE quality control tool for elevated throughput sequence data. Your Java What A match Java Runtime Ecology This Picard BAM/SAM Libraries (included in download) Code Maturation Robust. Mature code, but feedback exists comprehended. Code Released No, under GPL v3 or later. Initial Contact Simon Andrews Download Now Views…

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Bioconductor – scFeatures (development version)

DOI: 10.18129/B9.bioc.scFeatures   This is the development version of scFeatures; for the stable release version, see scFeatures. scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction Bioconductor version: Development (3.18) scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations…

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mbedtls_platform_support – Rust

Docs.rs mbedtls-platform-support-0.1.0 mbedtls-platform-support 0.1.0 Permalink Docs.rs crate page Apache-2.0 OR GPL-2.0-or-later Links Documentation Repository Crates.io Source Owners mzohreva Dependencies cfg-if ^1.0.0 normal chrono ^0.4 normal mbedtls-sys-auto ^2.25.0 normal spin ^0.4.0 normal cc ^1.0 build chrono ^0.4 normal Versions 75% of the crate is documented Platform x86_64-unknown-linux-gnu i686-unknown-linux-gnu Feature flags Rust…

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mbedtls-platform-support 0.1.0 on Cargo – Libraries.io

This is an idiomatic Rust wrapper for MbedTLS, allowing you to use MbedTLS with only safe code while being able to use such great Rust features like error handling and closures. Additionally, building on MbedTLS’s focus on embedded use, this crate can be used in a no_std environment. Building This…

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Bioconductor – magrene (development version)

DOI: 10.18129/B9.bioc.magrene   This is the development version of magrene; for the stable release version, see magrene. Motif Analysis In Gene Regulatory Networks Bioconductor version: Development (3.18) magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan…

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Bioconductor – miRSM

DOI: 10.18129/B9.bioc.miRSM   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see miRSM. Inferring miRNA sponge modules in heterogeneous data Bioconductor version: 3.16 The package aims to identify miRNA sponge modules in heterogeneous data. It provides several functions to study miRNA sponge modules, including…

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Bioconductor – pulsedSilac

DOI: 10.18129/B9.bioc.pulsedSilac     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see pulsedSilac. Analysis of pulsed-SILAC quantitative proteomics data Bioconductor version: 3.12 This package provides several tools for pulsed-SILAC data analysis. Functions are provided to organize the data, calculate isotope ratios, isotope fractions,…

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Bioconductor – SpatialDecon

DOI: 10.18129/B9.bioc.SpatialDecon     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SpatialDecon. Deconvolution of mixed cells from spatial and/or bulk gene expression data Bioconductor version: 3.12 Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation….

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Bioconductor – Vega

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see Vega. An R package for copy number data segmentation Bioconductor version: 2.11 Vega (Variational Estimator for Genomic Aberrations) is an algorithm that adapts a very popular variational model (Mumford and Shah) used in…

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Bioconductor – scDDboost

DOI: 10.18129/B9.bioc.scDDboost   A compositional model to assess expression changes from single-cell rna-seq data Bioconductor version: Release (3.17) scDDboost is an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions. Compared to other methods that assess differential expression, scDDboost benefits uniquely from information…

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tc6387xb.c source code [linux/drivers/mfd/tc6387xb.c] – Codebrowser

1 // SPDX-License-Identifier: GPL-2.0-only 2 /* 3 * Toshiba TC6387XB support 4 * Copyright (c) 2005 Ian Molton 5 * 6 * This file contains TC6387XB base support. 7 */ 8 9 #include <linux/module.h> 10 #include <linux/platform_device.h> 11 #include <linux/clk.h> 12 #include <linux/err.h> 13 #include <linux/mfd/core.h> 14 #include <linux/mfd/tmio.h> 15…

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Bioconductor – biomformat – rbiom: Read/Write, Transform, and Summarize ‘BIOM’ Data

DOI: 10.18129/B9.bioc.biomformat     This package is for version 3.8 of Bioconductor; for the stable, up-to-date released release, checkbiomformat. An interface package for the BIOM file format Bioconductor version: 3.8 This is an R packages for interfacing from the BIOM format. This package inclusive bottom tools since reading biom-format files,…

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Bioconductor – rSWeeP

DOI: 10.18129/B9.bioc.rSWeeP   Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences Bioconductor version: Release (3.17) The SWeeP method was developed to favor the analizes between amino acids sequences and to assist alignment free phylogenetic studies. This method is based on the concept of sparse words,…

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Bioconductor – lmdme

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see lmdme. Linear Model decomposition for Designed Multivariate Experiments Bioconductor version: 2.12 linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation,…

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Citing data privacy, GitLab syncs with Google generative AI

GitLab‘s partnership with Google for generative AI looks to assuage enterprise concerns about data privacy, but many open questions about licensing and other risks remain. The partnership news this week comes amid a tidal wave of IT products that incorporate generative AI built on large language models (LLM). Such…

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Bioconductor – TDbasedUFEadv

DOI: 10.18129/B9.bioc.TDbasedUFEadv   Advanced package of tensor decomposition based unsupervised feature extraction Bioconductor version: Release (3.17) This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics…

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Bioconductor – SICtools

DOI: 10.18129/B9.bioc.SICtools     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SICtools. Find SNV/Indel differences between two bam files with near relationship Bioconductor version: 3.12 This package is to find SNV/Indel differences between two bam files with near relationship in a way…

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Bioconductor – LBE

Estimation of the false discovery rate. Bioconductor version: 2.7 LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis….

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Bioconductor – ReUseData

DOI: 10.18129/B9.bioc.ReUseData   Reusable and reproducible Data Management Bioconductor version: Release (3.17) ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of…

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Bioconductor – IMAS

DOI: 10.18129/B9.bioc.IMAS     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see IMAS. Integrative analysis of Multi-omics data for Alternative Splicing Bioconductor version: 3.12 Integrative analysis of Multi-omics data for Alternative splicing. Author: Seonggyun Han, Younghee Lee Maintainer: Seonggyun Han <hangost at ssu.ac.kr>…

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Bioconductor – speckle

DOI: 10.18129/B9.bioc.speckle   Statistical methods for analysing single cell RNA-seq data Bioconductor version: Release (3.17) The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of…

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Bioconductor – MouseThymusAgeing

DOI: 10.18129/B9.bioc.MouseThymusAgeing     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MouseThymusAgeing. Single-cell Transcriptomics Data of the Ageing Mouse Thymus Bioconductor version: 3.13 This package provides data access to counts matrices and meta-data for single-cell RNA sequencing data of thymic epithlial cells…

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Bioconductor – GENIE3

DOI: 10.18129/B9.bioc.GENIE3     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see GENIE3. GEne Network Inference with Ensemble of trees Bioconductor version: 3.12 This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data. Author: Van Anh Huynh-Thu, Sara Aibar,…

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Bioconductor – retrofit (development version)

DOI: 10.18129/B9.bioc.retrofit   This is the development version of retrofit; to use it, please install the devel version of Bioconductor. RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics Bioconductor version: Development (3.17) RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without…

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Bioconductor – OutSplice (development version)

DOI: 10.18129/B9.bioc.OutSplice   This is the development version of OutSplice; to use it, please install the devel version of Bioconductor. Comparison of Splicing Events between Tumor and Normal Samples Bioconductor version: Development (3.17) An easy to use tool that can compare splicing events in tumor and normal tissue samples using…

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Novel rRNA transcriptional activity of NhaR revealed by its growth recovery for the bipA-deleted Escherichia coli at low temperature

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Bioconductor – TOP (development version)

DOI: 10.18129/B9.bioc.TOP   This is the development version of TOP; to use it, please install the devel version of Bioconductor. TOP Constructs Transferable Model Across Gene Expression Platforms Bioconductor version: Development (3.17) TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be…

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Bioconductor – eegc

DOI: 10.18129/B9.bioc.eegc     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see eegc. Engineering Evaluation by Gene Categorization (eegc) Bioconductor version: 3.12 This package has been developed to evaluate cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic…

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Bioconductor – RDRToolbox

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see RDRToolbox. A package for nonlinear dimension reduction with Isomap and LLE. Bioconductor version: 2.11 A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing…

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Bioconductor – diffHic

DOI: 10.18129/B9.bioc.diffHic     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see diffHic. Differential Analyis of Hi-C Data Bioconductor version: 3.15 Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts….

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Bioconductor – EDDA

DOI: 10.18129/B9.bioc.EDDA     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 EDDA. Experimental…

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Bioconductor – Sushi

DOI: 10.18129/B9.bioc.Sushi     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see Sushi. Tools for visualizing genomics data Bioconductor version: 3.14 Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures Author: Douglas H Phanstiel <dphansti at stanford.edu> Maintainer: Douglas H Phanstiel <dphansti…

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Bioconductor – SeqArray

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see SeqArray. Big Data Management of Whole-genome Sequence Variant Calls Bioconductor version: 3.4 Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls)…

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Bioconductor – DESpace (development version)

DOI: 10.18129/B9.bioc.DESpace   This is the development version of DESpace; to use it, please install the devel version of Bioconductor. DESpace: a framework to discover spatially variable genes Bioconductor version: Development (3.17) Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses….

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Bioconductor – SharedObject

DOI: 10.18129/B9.bioc.SharedObject     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SharedObject. Sharing R objects across multiple R processes without memory duplication Bioconductor version: 3.12 This package is developed for facilitating parallel computing in R. It is capable to create an R…

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List of all items in this crate

Docs.rs mbedtls-0.8.1 mbedtls 0.8.1 Permalink Docs.rs crate page Apache-2.0/GPL-2.0+ Links Documentation Repository Crates.io Source Owners github:fortanix:crates-owners Dependencies bit-vec ^0.5 normal bitflags ^1 normal block-modes ^0.3 normal byteorder ^1.0.0 normal cfg-if ^1.0.0 normal core_io ^0.1 normal mbedtls-sys-auto ^2.25.0 normal num-bigint ^0.2 normal rc2 ^0.3 normal serde ^1.0.7 normal serde_derive ^1.0.7 normal…

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Bioconductor – GeneRegionScan

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see GeneRegionScan. GeneRegionScan Bioconductor version: 2.11 A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since…

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Bioconductor – limmaGUI

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see limmaGUI. GUI for limma package with two color microarrays Bioconductor version: 3.3 A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package. Author: James Wettenhall [aut], Gordon…

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Bioconductor – curatedBreastData

DOI: 10.18129/B9.bioc.curatedBreastData     Curated breast cancer gene expression data with survival and treatment information Bioconductor version: Release (3.6) Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum…

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[PATCHv2 08/12] power: supply: generic-adc-battery: use simple-battery API

[PATCHv2 08/12] power: supply: generic-adc-battery: use simple-battery API – Sebastian Reichel From: Sebastian Reichel <sre@kernel.org> To: Sebastian Reichel <sre@kernel.org> Cc: Linus Walleij <linus.walleij@linaro.org>, Matti Vaittinen <mazziesaccount@gmail.com>, Rob Herring <robh+dt@kernel.org>, Krzysztof Kozlowski <krzysztof.kozlowski+dt@linaro.org>, linux-kernel@vger.kernel.org, linux-pm@vger.kernel.org, devicetree@vger.kernel.org Subject: [PATCHv2 08/12] power: supply: generic-adc-battery: use simple-battery API Date: Tue, 14 Mar 2023 23:55:31…

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Pytorch failed after opencv installation – Python

dongho March 11, 2023, 8:11am 1 My python system is anaconda on ubuntu 22.04. If I install pytorch after installing opencv, pytorch cuda stops working. torch.cuda.is_available()False Pytorch worked well before I installed opencv. If I install opencv after installing pytorch, it takes so much time than usual. Sometimes it returns…

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[PATCH v2 5/9] coresight: Dynamically add connections

[PATCH v2 5/9] coresight: Dynamically add connections – James Clark From: James Clark <james.clark@arm.com> To: coresight@lists.linaro.org Cc: James Clark <james.clark@arm.com>, Mathieu Poirier <mathieu.poirier@linaro.org>, Suzuki K Poulose <suzuki.poulose@arm.com>, Mike Leach <mike.leach@linaro.org>, Leo Yan <leo.yan@linaro.org>, Alexander Shishkin <alexander.shishkin@linux.intel.com>, linux-arm-kernel@lists.infradead.org, linux-kernel@vger.kernel.org Subject: [PATCH v2 5/9] coresight: Dynamically add connections Date: Fri, 10 Mar…

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Bioconductor – SpidermiR

DOI: 10.18129/B9.bioc.SpidermiR     SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data Bioconductor version: Release (3.6) The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in…

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Bioconductor – BG2 (development version)

DOI: 10.18129/B9.bioc.BG2   This is the development version of BG2; to use it, please install the devel version of Bioconductor. Performs Bayesian GWAS analysis for non-Gaussian data using BG2 Bioconductor version: Development (3.17) This package is built to perform GWAS analysis for non-Gaussian data using BG2. The BG2 method uses…

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Bioconductor – GEOquery

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see GEOquery. Get data from NCBI Gene Expression Omnibus (GEO) Bioconductor version: 2.9 The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this…

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Bioconductor – ASEB

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see ASEB. Predict Acetylated Lysine Sites Bioconductor version: 2.13 ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT-family. Author: Likun Wang <wanglikun at tsinghua.edu.cn> and Tingting…

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Bioconductor – speckle (development version)

DOI: 10.18129/B9.bioc.speckle   This is the development version of speckle; to use it, please install the devel version of Bioconductor. Statistical methods for analysing single cell RNA-seq data Bioconductor version: Development (3.17) The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains…

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[PATCH 8/8] clk: Add KUnit tests for clks registered with struct clk_parent_data

[PATCH 8/8] clk: Add KUnit tests for clks registered with struct clk_parent_data – Stephen Boyd From: Stephen Boyd <sboyd@kernel.org> To: Michael Turquette <mturquette@baylibre.com>, Stephen Boyd <sboyd@kernel.org> Cc: linux-kernel@vger.kernel.org, linux-clk@vger.kernel.org, patches@lists.linux.dev, Brendan Higgins <brendan.higgins@linux.dev>, David Gow <davidgow@google.com>, Greg Kroah-Hartman <gregkh@linuxfoundation.org>, “Rafael J . Wysocki” <rafael@kernel.org>, Richard Weinberger <richard@nod.at>, Anton Ivanov <anton.ivanov@cambridgegreys.com>,…

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Bioconductor – Doscheda

DOI: 10.18129/B9.bioc.Doscheda     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Doscheda. A DownStream Chemo-Proteomics Analysis Pipeline Bioconductor version: 3.13 Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass…

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Scope for making LAMMPS Automatically Differentiable – LAMMPS Development

Dear LAMMPS developers, With the growing use of machine learning and optimization techniques (that are powered by automatic differentiation Automatic differentiation – Wikipedia), and their adoption and use in the field of molecular modelling, I thought it could be worth discussing whether making LAMMPS – a very efficient, flexible, and…

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Bioconductor – GOsummaries

DOI: 10.18129/B9.bioc.GOsummaries     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see GOsummaries. Word cloud summaries of GO enrichment analysis Bioconductor version: 3.12 A package to visualise Gene Ontology (GO) enrichment analysis results on gene lists arising from different analyses such clustering or…

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Bioconductor – crisprseekplus

DOI: 10.18129/B9.bioc.crisprseekplus     crisprseekplus Bioconductor version: Release (3.16) Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis. Author: Sophie Wigmore <Sophie.Wigmore at umassmed.edu>, Alper Kucukural <alper.kucukural at umassmed.edu>, Lihua Julie Zhu <julie.zhu at umassmed.edu>, Michael Brodsky <Michael.Brodsky at umassmed.edu>, Manuel Garber <Manuel.Garber…

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dfl-fme-pr.c source code [linux/drivers/fpga/dfl-fme-pr.c] – Codebrowser

1 // SPDX-License-Identifier: GPL-2.0 2 /* 3 * Driver for FPGA Management Engine (FME) Partial Reconfiguration 4 * 5 * Copyright (C) 2017-2018 Intel Corporation, Inc. 6 * 7 * Authors: 8 * Kang Luwei <luwei.kang@intel.com> 9 * Xiao Guangrong <guangrong.xiao@linux.intel.com> 10 * Wu Hao <hao.wu@intel.com> 11 * Joseph Grecco…

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Explore SageMath with the SmartNoteBook

Explore SageMath with the SmartNoteBook Drawn by Using SageMath About SageMath SageMath is a free, open-source mathematical software system under the GPL. It integrates many open source Python packages and is written in Python, but also supports other languages. Its goal is to create a mutable open source software alternative…

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Bioconductor – ScaledMatrix

DOI: 10.18129/B9.bioc.ScaledMatrix     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ScaledMatrix. Creating a DelayedMatrix of Scaled and Centered Values Bioconductor version: 3.13 Provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale()…

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Bioconductor – PathoStat

DOI: 10.18129/B9.bioc.PathoStat     PathoStat Statistical Microbiome Analysis Package Bioconductor version: Release (3.11) The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts,…

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Bioconductor – MIRA

DOI: 10.18129/B9.bioc.MIRA     Methylation-Based Inference of Regulatory Activity Bioconductor version: Release (3.15) DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and…

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Bioconductor – ExiMiR

DOI: 10.18129/B9.bioc.ExiMiR     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ExiMiR. R functions for the normalization of Exiqon miRNA array data Bioconductor version: 3.12 This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA…

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Bioconductor – gcapc

DOI: 10.18129/B9.bioc.gcapc     GC Aware Peak Caller Bioconductor version: Release (3.13) Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation. Author: Mingxiang Teng and…

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[PATCH AUTOSEL 4.19 1/6] ASoC: cs42l56: fix DT probe

[PATCH AUTOSEL 4.19 1/6] ASoC: cs42l56: fix DT probe * [PATCH AUTOSEL 4.19 1/6] ASoC: cs42l56: fix DT probe @ 2023-02-09 11:19 Sasha Levin 2023-02-09 11:19 ` [PATCH AUTOSEL 4.19 2/6] tools/virtio: fix the vringh test for virtio ring changes Sasha Levin ` (4 more replies) 0 siblings, 5 replies;…

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