Publications by Shenfeng Qiu
ssbm_4_samples_integrated
Edited by Shenfeng Qiu 07232023 CAN RUN ALL BLOCK BY BLOCK BEAUTIFULLY, INCLUDING MONOCLE3, AZIMUTH MAPPING AND SHINYCELL VISUALIZATION with reference to: https://satijalab.org/seurat/articles/integration_introduction.html Import Group samples Quality Control Plot Data Joint filtering effects: After subseting, I only keep those genes expresse...
2684 sym 53 img
Anndata file manipulation
Download Example Tabula Sapiens Anndata Object and Manipulation !wget https://figshare.com/ndownloader/files/34701991 # not working with Anaconda terminal, has to be wsl terminal The following block will download the TS_lung.h5ad file into current directory import requests from zipfile import ZipFile from io import BytesIO # Downloading the fi...
379 sym Python (10038 sym/49 pcs) 5 tbl
Simple Volcano plot for seurat .csv file
Reference: https://bioconductor.org/packages/devel/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html#download-the-package-from-bioconductor # use the next block for plotting # Load required libraries library(ggplot2) library(dplyr) ## ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ## ## ...
389 sym R (9480 sym/19 pcs) 10 img
human bone marrow sample
#load seurat package and dependencies library(dplyr) library(Seurat) library(patchwork) library(cowplot) library(ggplot2) library(rstatix) library(RColorBrewer) setwd("D:/Bioinformatics Projects/shalini_bm_noe15") load NoE15 dataset # read the NoE15 sample NoE15.data <- Read10X(data.dir = "NoE15/outs/filtered_feature_bc_matrix/") dim(NoE1...
1061 sym R (28293 sym/149 pcs) 22 img
ss_one_bone_marrow_E15
#load seurat package and dependencies library(dplyr) library(Seurat) ## Warning: package 'Seurat' was built under R version 4.2.2 library(patchwork) library(cowplot) library(ggplot2) ## Warning: package 'ggplot2' was built under R version 4.2.1 library(rstatix) library(RColorBrewer) setwd("D:/Bioinformatics Projects/shalini_bm") load E15 datas...
1067 sym R (28008 sym/157 pcs) 22 img
bulk RNAseq analysis - mouse brain tissue
SQ NOTE: use this to process the mouse bulk RNAseq data, three FAD vs three Ctrl samples. can run all, no problem. By default, the ctrl (ref) samples will be on the left side of the csv file, and fad sample on the right side of csv file. if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::insta...
389 sym R (18152 sym/94 pcs) 3 img
DESeq bulk analysis online tutorial
https://genviz.org/module-04-expression/0004/02/01/DifferentialExpression/ SQ NOTE: can run ALL library(DESeq2) ## Loading required package: S4Vectors ## Loading required package: stats4 ## Loading required package: BiocGenerics ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:stats': ## ## IQR, ma...
216 sym R (49872 sym/107 pcs) 9 img
Another DESeq2 tutorial from counting matrix
Source https://lashlock.github.io/compbio/R_presentation.html SQ NOTE: can run ALL library(DESeq2) ## Loading required package: S4Vectors ## Loading required package: stats4 ## Loading required package: BiocGenerics ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:stats': ## ## IQR, mad, sd, var, xt...
507 sym R (10619 sym/55 pcs) 3 img
bulk RNAseq analysis
SQ NOTE: All block can run library(DESeq2) library(ggplot2) library(ComplexHeatmap) library("org.Hs.eg.db") ls ## HS_STAR_dir ## Homo_sapiens.GRCh38.109.gtf ## Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa ## Sanbomics_RNAseq_video6.ipynb ## bams ## count.out ## count.out.summary ## count_table.csv ## deseq_results.csv ## deseq_workspa...
126 sym R (57750 sym/64 pcs) 4 img
Signac_PMBC_10K
For this tutorial, we will be analyzing a single-cell ATAC-seq dataset of human peripheral blood mononuclear cells (PBMCs) provided by 10x Genomics. The following files are used in this vignette, all available through the 10x Genomics website: The Raw data The Metadata The fragments file The fragments file index View data download code To...
17043 sym R (17993 sym/48 pcs) 9 img