ATpoint
/ getPercentExpression.R
Last active
October 15, 2024 13:38
Efficient calculation of percentage of expression per cluster, for example for scRNA-seq.
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| #' Given a matrix-like object with genes being rows, samples/cells being columns, | |
| #' and a group information for the columns, calculate the percentage of expression per group. | |
| #' No dependencies other than base R. The CsparseMatrix format, commonly used in scRNA-seq is supported. | |
| #' | |
| #' @param data numeric matrix or data.frame-like object | |
| #' @param group a vector (character or factor) | |
| #' @param threshold values above this threshold are considered expressed | |
| #' @param digits round results to this number of digits | |
| #' | |
| #' @examples |
ATpoint
/ biostars_maplots_deseq2.R
Created
August 14, 2021 20:14
https://www.biostars.org/p/9484986/#9485061
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| library(DESeq2) | |
| #/ from https://raw.githubusercontent.com/shangguandong1996/picture_link/main/WFX_count_Rmatrix.txt | |
| data <- read.delim("WFX_count_Rmatrix.txt", row.names = "Geneid") | |
| get_res <- function(dds){ | |
| dds <- DESeq(dds) | |
| res <- results(dds, name=resultsNames(dds)[2]) | |
| lfcShrink(dds, coef=resultsNames(dds)[2], res=res, type="ashr") | |
| } |
ATpoint
/ compilation_chromap.txt
Created
June 21, 2021 09:57
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| $ make | |
| mkdir -p objs | |
| g++ -std=c++11 -Wall -O3 -fopenmp -march=native -c src/chromap.cc -o objs/chromap.o -lm -lz | |
| src/chromap.cc:1096:0: warning: ignoring #pragma omp taskloop [-Wunknown-pragmas] | |
| #pragma omp taskloop grainsize(grain_size) //num_tasks(num_threads_* 50) | |
| ^ | |
| src/chromap.cc:2001:0: warning: ignoring #pragma omp taskloop [-Wunknown-pragmas] | |
| #pragma omp taskloop num_tasks(num_threads_* num_threads_) | |
| ^ | |
| src/chromap.cc: In instantiation of 'void chromap::Chromap<MappingRecord>::MapSingleEndReads() [with MappingRecord = chromap::PAFMapping]': |
ATpoint
/ stdout_problem.nf
Last active
June 8, 2021 19:41
Problem: .nextflow.out piles up the entire stdout channel, feels like it should not do that when output is explicitely stdout
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| #!/usr/bin/env nextflow | |
| nextflow.enable.dsl=2 | |
| // Dummy example: Decompress a BAM in processA => stdout => read in processB as stdin and compress back to BAM. | |
| process processA { | |
| input: | |
| path(bam) |
ATpoint
/ renv_example_biostars498049
Last active
May 12, 2021 08:22
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| $ head renv.lock -n 40 | |
| { | |
| "R": { | |
| "Version": "4.0.3", | |
| "Repositories": [ | |
| { | |
| "Name": "CRAN", | |
| "URL": "https://cran.rstudio.com" | |
| } | |
| ] |
ATpoint
/ edgeR_TMM_vs_naive.R
Last active
April 19, 2021 23:53
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| library(recount) | |
| library(edgeR) | |
| #/ Get the counts from GTEx via recount as a SummarizedExperiment | |
| #/ => 1.3GB file | |
| options(timeout=600) | |
| download_study("SRP012682", type = "rse-gene") | |
| load(file.path("SRP012682", "rse_gene.Rdata")) | |
| #/ remove whitespaces in tissue names: |
ATpoint
/ error_SE_54678805
Created
April 17, 2021 11:46
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| FATAL: container creation failed: unable to copy files to container fs: while copying [environment.yml] to /tmp/rootfs-4b4c7b49-9f72-11eb-a808-12cf446d2005/environment.yml: exit status 1: /bin/cp: cannot stat 'environment.yml': No such file or directory | |
| FATAL: While performing build: while running engine: while running /usr/local/libexec/singularity/bin/starter: exit status 255 | |
| FATAL: While performing build: build image size <= 0 |
ATpoint
/ sessioninfo_2021_02_03.txt
Created
February 3, 2021 20:37
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| > sessionInfo() | |
| R version 4.0.3 (2020-10-10) | |
| Platform: x86_64-apple-darwin17.0 (64-bit) | |
| Running under: macOS Mojave 10.14.6 | |
| Matrix products: default | |
| BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib | |
| LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib | |
| locale: |
ATpoint
/ guides_angles.R
Last active
September 24, 2021 10:35
No more messing with h/vjust when rotating labels
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| library(ggplot2) | |
| library(reshape2) | |
| library(egg) | |
| # thanks to https://stackoverflow.com/questions/1330989/rotating-and-spacing-axis-labels-in-ggplot2/60650595#60650595 | |
| dat<-reshape2::melt(data.frame(groupA=rnorm(20), | |
| groupB=rnorm(20), | |
| groupC=rnorm(20))) |
ATpoint
/ compilation_error.txt
Created
November 27, 2020 15:26
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| metaBigBam.c:485:12: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] | |
| if (h->cigar_tab == 0) | |
| ^ | |
| /usr/local/include/htslib/sam.h:75:29: note: 'cigar_tab' has been explicitly marked deprecated here | |
| const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | |
| ^ | |
| /usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED' | |
| #define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message))) | |
| ^ | |
| metaBigBam.c:487:5: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] |