Tag: DESC

I have been training my custom Image classification model on the PyTorch transformers library to deploy to hugging face however, I cannot figure out how to export the model in the correct format for HuggingFace with its respective config.json file. I’m new to PyTorch and AI so any help would…

I’m looking for a way to arrange the bar plot produced with ggplot2 by descending order of “utsugds2gp_22(happy condition)” that equal to 1 (category=not happy) within each scode1_22 group (area). The original bar plot I generated is below: My codes are as following : fill <- c(“white”, “#E1B378”) ka %>%…

[This article was first published on pacha.dev/blog, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. R and Shiny Training: If you find this…

fGSEA collapsePathways function not working 0 Hello all, I’m running the package fgsea and I’m having trouble with the collapsePathways function. When not using that function, I get the expected data frame with 8 columns (pathway, pval, NES, etc.) that I can then plot using ggplot. However, when I try…

Introduction Welcome to this hands-on guide to fine-tuning image classifiers with PyTorch and the timm library! Fine-tuning refers to taking a pre-trained model and adjusting its parameters using a new dataset to enhance its performance on a specific task. We can leverage pre-trained models to achieve high performance even when…

[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…

I’m very sorry for my poor knowledge here but I think I’m missing something here.. I want to generate OpenAPI docs to my .net core web app. I also want to use versions for my methods. So I do it like this [ApiController] [Route(“v{version:apiVersion}/Do”)] public class DoController : ControllerBase {…

I am trying to generate as much code as possible for application using OpenAPI generator. Some of the requests are get with support for paging and sorting. Using spring it is easy to create @GetMapping(“/snakes”) public ResponseEntity<List<Snake>> findAll(Pageable pageable) This makes the /snakes endpoint to support paging and sorting using…

This question was caused by a typo or a problem that can no longer be reproduced. While similar questions may be on-topic here, this one was resolved in a way less likely to help future readers. While trying to knit my RMarkdown I got this…

Hello, I performed an alignment using hmmer hmmsearch tool using metagenomic contigs as a query and a hydrocarbon database (hydrocarbon.hmm file). I n first instance I first retrieved all ORFs from the contigs and translated them with esl-translate program as following: esl-translate -c 11 input_contigs.fa > translated_orfs.fa After getting the…

We use OpenAPI to generate the interface description for the services exposed in one of our server applications. We use that openapi.yaml then to generate client-sided libraries that will interact with these services for various languages. As the server backend uses the typical Maven + Java Spring Boot techstack we…

We are looking for pathogen miRNAs in host tissues among reads that couldn’t map to the host genome. The relevant commands are below; mapper.pl “$file”_HOST_UNMAPPED.fq -e -h -m -p $PathogenGenomeBasename -t “$file”_HOST_UNMAPPED_vs_PATHOGEN.arf -v -s “$file”_HOST_UNMAPPED_vs_PATHOGEN_COLLAPSED.fa miRDeep2.pl “$file”_HOST_UNMAPPED_vs_PATHOGEN_COLLAPSED.fa $PathogenGenomeBasename.fa HOST_UNMAPPED_vs_PATHOGEN.arf $PathogenMatureMiRNA $PathogenMiRNA $PathogenPrecursorMiRNA -c -d -g -1 According to this analysis…

al3xh May 3, 2023, 2:41pm 1 I’m attempting to build a pytorch v1.4 wheel using the instructions found here but am running into some issues that I believe is due to cuDNN being version 8.0 instead of 7.0. For example: ../caffe2/operators/conv_op_cudnn.cc:1173:11: error: ‘CUDNN_CONVOLUTION_BWD_FILTER_SPECIFY_WORKSPACE_LIMIT’ was not declared in this scope CUDNN_CONVOLUTION_BWD_FILTER_SPECIFY_WORKSPACE_LIMIT,…

Hey all, I am trying to run this script in R but due to some reason I am getting the following error, I don’t know what I am missing. Any help would be appreciated. library(“tidyverse”) library(“ggrepel”) library(“dplyr”) df |> dplyr::mutate( label=ifelse( avg_log2FC >= nth(avg_log2FC, 10, desc(avg_log2FC)) | avg_logFC <= nth(avg_log2FC,…

From Linus Walleij <> Date Mon, 01 May 2023 11:05:21 +0200 Subject [PATCH 1/3] ARM/gpio: Push OMAP2 quirk down into TWL4030 driver The TWL4030 GPIO driver has a custom platform data .set_up()callback to call back into the platform and do misc stuff suchas hog and export a GPIO for WLAN…

I have a dataframe in R #creating a dataset codigo <- paste0(“COD”, sprintf(“%03d”, 1:4)) vgene <- paste0(“VG”, LETTERS[1:8]) set.seed(123) codigo <- sample(codigos, 40, replace = TRUE) vgene <- sample(vgene, 40, replace = TRUE) datos_vgene <- data.frame(codigo, vgene) codigo vgene 1 COD001 VGG 2 COD002 VGG 3 COD003 VGC 4 COD004…

From Linus Walleij <> Date Mon, 01 May 2023 11:05:22 +0200 Subject [PATCH 2/3] ARM: omap2: Get USB hub reset GPIO from descriptor This switches the USB hub GPIO reset line handling in theOMAP2 pdata quirks over to using GPIO descriptors to avoid usingthe global GPIO numberspace.Since the GPIOs are…

p-fold plot 1 I want to construct this plot, and I have already performed the DESeq analysis. This is how the data looks: Gene p_val avg_logFC pct.1 pct.2 p_val_adj HLA-B 1.69E-152 0.719935845 0.993 0.988 2.38E-148 VAMP5 2.73E-97 1.137804386 0.87 0.527 3.85E-93 PSME2 6.25E-88 0.820693535 0.965 0.88 8.80E-84 STAT1 1.03E-83 0.890453249…

I want to add labels to my ggplot graph. The graph was created with the “freq” column, which contains the previously calculated percentage values. At the top of the graph, I want to add the sum per group of the “n” variable instead of the predefined variable. I have had…

Introduction Building web APIs using the REST architectural style can help us create well structured and efficient APIs for our web applications. However, it can be difficult to apply effectively. If we want to build a REST API with Node.js, we’ll typically start by designing the API interface, integrating a…

[PATCH v6 07/13] coresight: Store pointers to connections rather than an array of them – James Clark From: James Clark <james.clark@arm.com> To: coresight@lists.linaro.org, quic_jinlmao@quicinc.com, mike.leach@linaro.org, suzuki.poulose@arm.com Cc: James Clark <james.clark@arm.com>, Leo Yan <leo.yan@linaro.org>, Alexander Shishkin <alexander.shishkin@linux.intel.com>, Mathieu Poirier <mathieu.poirier@linaro.org>, Greg Kroah-Hartman <gregkh@linuxfoundation.org>, linux-arm-kernel@lists.infradead.org, linux-kernel@vger.kernel.org Subject: [PATCH v6 07/13] coresight: Store…

Source: geoalchemy2 Version: 0.13.1-2 Severity: serious Tags: sid bookworm bookworm-ignore User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of geoalchemy2 the autopkgtest of geoalchemy2 fails in testing on s390x when that autopkgtest is run with the binary packages of geoalchemy2 from unstable. It passes when run with only…

I have a dataframe, that I want to use to plot a bar plot. The numeric variable is jumbled and I sorted it into descedning order. I want to plot the new sorted dataframe using ggplot but the barplot is not giving me the desired output. Name <- c(“Jon”, “Bill”,…

I have seen this issue being recurrent and tried many options for the last two days but non yielded to correct installation of any of these packages. I used BiocManager as suggested in other issues, also tried to install from local source, nothing seems to be working. This issue started…

Since there is not statistics involved in the question, I think it belongs in the stackexchange where I see most R questions. I don’t know how to port the question so I will let someone else do it. But here is the solution – which might be less readable than…

From GeneSetEnrichmentAnalysisWiki GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact Introduction With the release of MSigDB 2023.1 we have created a new SQLite database for the fully annotated gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Ms) resources. Each ships as a single-file database…

php generating a large file of api specification on localhost:8080/api/openapi but when ever first time it load returns 404 error . swagger ui javascript framework is use to consume api specifications window.onload = function() { //<editor-fold desc=”Changeable Configuration Block”> // the following lines will be replaced by docker/configurator, when it…

[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…

ADC Therapeutics SA 2022 Annual Report Table of Contents Letter to Shareholders Business Update Financial Review Corporate Governance Report from the Auditor on the Consolidated IFRS Financial Statements Consolidated IFRS Financial Statements for the Year Ended December 31, 2022 Report from the Auditor on the Statutory Financial Statements of ADC…

Hi, I am on bullseye and am trying to install the package r-cran-ggplot2. This fails with E: Failed to fetch deb.debian.org/debian/pool/main/p/postgresql-13/libpq5_13.8-0%2bdeb11u1_amd64.deb 404 Not Found [IP: 146.75.122.132 80] (full output below). There seems to be a dependency on libpq5 version 13.8 whereas the version available for bullseye is 13.9. Any ideas how to…

[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…

[PATCH v1 2/2] media: lm3560: convent to OF – Svyatoslav Ryhel From: Svyatoslav Ryhel <clamor95@gmail.com> To: Mauro Carvalho Chehab <mchehab@kernel.org>, Rob Herring <robh+dt@kernel.org>, Krzysztof Kozlowski <krzysztof.kozlowski+dt@linaro.org>, Svyatoslav Ryhel <clamor95@gmail.com>, Hans Verkuil <hverkuil-cisco@xs4all.nl>, Luca Ceresoli <luca.ceresoli@bootlin.com>, Jean Delvare <jdelvare@suse.de>, Sebastian Reichel <sebastian.reichel@collabora.com>, Daniel Jeong <gshark.jeong@gmail.com>, Ldd-Mlp <ldd-mlp@list.ti.com> Cc: linux-media@vger.kernel.org, devicetree@vger.kernel.org, linux-kernel@vger.kernel.org…

I am training PyTorch model for binary classification and my input vector of length 561 [341 is one hot encoding] and the others are features between 0 and 1. my output is [0,1] or [1,0] . My issue is that the training loss is always decrease i tried to try…

[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>,…

I want to improve my chart on two different points. I don’t like the numbers on the bottom line so they have to be removed. I want the data label behind the chart and not half in it. Code for the calculation select f.ClubName, round(w.Waarde/w.Selectie,0) as Gem_waarde from fact f…

Learn how to run SQL in your Jupyter Notebooks Photo by Wafer WAN on Unsplash Traditionally, data scientists use Jupyter Notebook to pull data from database servers, or from external datasets (such as CSV, JSON files, etc) and store them into Pandas dataframes: All images by author unless otherwise stated…

Error in R: System command ‘Rcmd.exe’ failed 0 Hi all, I’m getting the following error when installing packages from github: devtools::install_github(“https://github.com/CostaLab/CrossTalkeR”, build_vignettes = TRUE) checking DESCRIPTION meta-information … – installing the package to build vignettes ———————————– ERROR: dependency ‘qpdf’ is not available for package ‘CrossTalkeR’ – removing ‘C:/Users/FNG-DA/AppData/Local/Temp/RtmpIlN5Iz/Rinst11e07cd110b5/CrossTalkeR’ ———————————– ERROR:…

I’m trying to setup some testing of our job_submit.lua plugin so I can verify that changes I make to it don’t break anything. I looked into luaunit for testing, and that seems like it would do what I need….let me set the value of inputs, call the slurm_job_submit()…

I have created a vector with the order of a dot plot mentioned but it doesn’t plot in that order/ Thanks for the suggestions. order <- sav %>% filter(Subject == “Food”) %>% arrange(desc(Percentage)) %>% select(Location) %>% unlist() %>% unname() order <- replace(order, c(1, 8), order[c(8, 1)]) sav %>% ggplot(aes(x =…

#include <stdio.h> #include <slurm/slurm.h> #include <slurm/slurm_errno.h> int main (int argc, char *argv[]) { job_desc_msg_t update_job_msg; step_update_request_msg_t update_step_msg; slurm_init_job_desc_msg( &update_job_msg ); update_job_msg.job_id = 1234; update_job_msg time_limit = 200; if (slurm_update_job (&update_job_msg)) { slurm_perror (“slurm_update_job error”); exit (1); } slurm_init_update_step_msg( &update_step_msg ); update_step_msg.job_id = 1234; update_step_msg.step_id = 2; update_step_msg time_limit = 30;…

Hi, I failed to install clusterProfiler on Mac M1. May I ask the solution >BiocManager::install(“clusterProfiler”) Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) ‘clusterProfiler’ also installing the dependencies ‘fgsea’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’ Warning: unable to access index for repository bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL ‘https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES’ Warning: unable to access…

I’m trying to use pytorch-lightning for token-classification model. I have already built a model for token classification without lightning. I’m confused on what changes should be done with existing code to integrate pytorch-lightning. Following is my pytorch code: model = BertForTokenClassification.from_pretrained( ‘bert-large-cased’, num_labels=len(tag2idx), output_attentions = False, output_hidden_states = False )…

[PATCH] mmc: atmel: convert to gpio descriptos * [PATCH] mmc: atmel: convert to gpio descriptos @ 2023-01-26 13:50 Arnd Bergmann 2023-01-26 23:54 ` Jakub Kicinski 2023-01-27 10:32 ` Nicolas Ferre 0 siblings, 2 replies; 4+ messages in thread From: Arnd Bergmann @ 2023-01-26 13:50 UTC (permalink / raw) To: Ludovic…

From: Arnd Bergmann <arnd@arndb.de> gpio_set_debounce() only has a single user, which is triviallyconverted to gpiod_set_debounce(). Signed-off-by: Arnd Bergmann <arnd@arndb.de>—Documentation/driver-api/gpio/legacy.rst | 2 —…/zh_CN/driver-api/gpio/legacy.rst | 1 –Documentation/translations/zh_TW/gpio.txt | 1 –drivers/input/touchscreen/ads7846.c | 25 ++++++++++———include/linux/gpio.h | 10 ——–5 files changed, 13 insertions(+), 26 deletions(-) diff –git a/Documentation/driver-api/gpio/legacy.rst b/Documentation/driver-api/gpio/legacy.rstindex a0559d93efd1..e0306e78e34b 100644— a/Documentation/driver-api/gpio/legacy.rst+++ b/Documentation/driver-api/gpio/legacy.rst@@ -238,8 +238,6…

Still working in my project with R. Here’s the code I have so far. # change columns to factors# dat[, 9:23] <- lapply(dat[, 9:23], factor, levels = c(1, 2, 3, 4), labels = c(“Nunca”, “1 vez por semana”, “3 veces o menos a la semana”, “Más de 4 veces a…

If it is necessary to swap the R plot axis, try to do that with the x and y arguments. Package ggplot2 allows you to swap the axis by using coord_flip, but it is mostly unnecessary. Try to fix the problem at the beginning. Swapping the ggplot2 axis might be…

Re: [PATCH 2/3] hwmon (coretemp): Add support for dynamic tjmax – Guenter Roeck From: Guenter Roeck <linux@roeck-us.net> To: Zhang Rui <rui.zhang@intel.com> Cc: jdelvare@suse.com, fenghua.yu@intel.com, linux-hwmon@vger.kernel.org, srinivas.pandruvada@linux.intel.com Subject: Re: [PATCH 2/3] hwmon (coretemp): Add support for dynamic tjmax Date: Fri, 11 Nov 2022 13:26:45 -0800 [thread overview] Message-ID: <20221111212645.GA1059539@roeck-us.net> (raw) In-Reply-To:…

I have data that includes the number of countries in each region per year in a data set. I have used the below code to plot a bar chart but I would like it to plot the numbers for each year but not sure how. region_year <- data_na_removed%>% group_by(Region, Year)%>%…

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

Savage, P. E., Brown, S., Sakai, E. & Currie, T. E. Statistical universals reveal the structures and functions of human music. Proc. Natl Acad. Sci. USA 112, 8987–8992 (2015). CAS  PubMed  PubMed Central  Article  Google Scholar  Ravignani, A., Delgado, T. & Kirby, S. Musical evolution in the lab exhibits rhythmic…

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

Use geom_point instead of geom_count because you’re getting the point sizes from a column in your table, not by counting the rows. Use scale_fill_manual to use the colours that are specified in your table. Use reorder when specifying the y variable in ggplot to reverse the order. TEST_df = tribble(~CellType,~name,~value,~size,~colour,…

[PATCH v2] media: m5mols: Convert to use GPIO descriptors * [PATCH v2] media: m5mols: Convert to use GPIO descriptors @ 2022-02-24 0:13 Linus Walleij 0 siblings, 0 replies; only message in thread From: Linus Walleij @ 2022-02-24 0:13 UTC (permalink / raw) To: Mauro Carvalho Chehab, linux-media Cc: Linus Walleij,…

How to convert transcript-relative coordinates to genomic coordinates? 0 I have queried using Entrez Utilities (efetch: www.ncbi.nlm.nih.gov/books/NBK25499/) and obtained annotations for transcripts like the following: >Feature ref|NM_152486.3| 1 2557 gene gene SAMD11 gene_syn MRS gene_desc sterile alpha motif domain containing 11 db_xref GeneID:148398 db_xref HGNC:HGNC:28706 db_xref MIM:616765 How/what database should…

I have a bed file which contains DNA sequences information as follow: ** track name=”194″ description=”194 methylation (sites)” color=0,60,120 useScore=1 chr1 15864 15866 FALSE 894 + chr1 534241 534243 FALSE 921 – chr1 710096 710098 FALSE 729 + chr1 714176 714178 FALSE 12 – chr1 720864 720866 FALSE 988 -…

I make an editor for own game engine and I used for 2d rendering Direct2D but I wanted to render a directx texture on window in editor, I didn’t find convenient way to convert directx texture to direct2d bitmap. I decided to make own 2d render on directx 11 and…

Research Fellow (Computational Biology, Bioinformatics, Machine Learning) – Career at NTU University in Singapore. Apply for NTU University job and get your career at NTU University! Company: NTU University Job Type: Full Time Work Place: Singapore Salary: SGD 10000 / Month Job Description A Research Fellow position is available in…

How can I rank the first 4 group of my dataframe associated to the highest value in the count column and create a 5th group summing up the remaining groups and their associated values ? What I did so far: dummy_dataframe <- data.frame(group = c(“A”, “B”, “A”, “A”, “C”, “C”,…

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: ampere2.nyi.freebsd.org/data/main-arm64-default/p7539e33f88ff_s169b368a62/logs/RStudio-2021.09.1+372.log Build URL: ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p7539e33f88ff_s169b368a62 Log: =>> Building devel/RStudio build started at Wed Dec 8…

README ggmatplot is a quick and easy way of plotting the columns of two matrices or data frames against each other using ggplot2. Overview ggplot2 requires wide format data to be wrangled into long format for plotting, which can be quite cumbersome when creating simple plots. Therefore, the motivation for…

# # Open AlphaFold database models for proteins larger than 1400 amino acids. # These calculated in 1400 amino acid segments every 200 amino acids due to # limitations (GPU memory) of the AlphaFold software. We load and align # the segment models. This produces many clashes. # # Opening…

Upon request, a quick tutorial for processing the Agilent micro-RNA (miRNA) microarray data of GSE28955. The raw TXT files are contained in: ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28955/suppl/GSE28955_RAW.tar Download this TAR file Unpack it [the TAR file] Unzip the txt.gz files Store these [txt files] in a directory raw/ Then, create a tab-delimited file, targets.txt,…

Differential Gene Expression after batch correction with DESC? 0 I recently performed batch effect correction on single cell RNA-seq data with DESC. www.nature.com/articles/s41467-020-15851-3#Sec11 eleozzr.github.io/desc/ The batch corrected clustering and dimensional reduction worked well but I would like to determine differentially expressed genes between cell populations from two different batches. I…