Bioinformatics

Prepare CRISPR/CAS9 gRNAs of non-coding elements for perturb-seq

crispr/cas9
grna
cre
perturb-seq
Use CRISPOR to generate candidate gRNAs of non-coding elements:
Dec 8, 2025
Rui Yang

Introduction to scOmics data structures

scomics
data structures
起始于 raw counts matrix。
Dec 8, 2025
Rui Yang

scanpy demo: preprocessing, clustering, and cell-type annotation

scanpy
demo
For convenience, see HTML or PDF.
Dec 8, 2025
Rui Yang

Visualization solutions in programming language level

visualization
r
python
julia
从一个完整的绘图单位 Figure（画布）开始，其可以包含多个 Axes（坐标系：直角坐标系、极坐标系），这是（堆叠）放置具体 plots（如散点图、曲线图等）的地方，每个 Axes 可以包含 2 个（2D - (x, y) or (theta, r)）或 3 个（3D - (x, y, z)）Axis，其指代具体的坐标轴。
Dec 8, 2025
Rui Yang

Methods for adding MT genome and annotation

MT genome
MT annotation
如果公共数据库（e.g., Ensembl, NCBI）存在目标物种的 MT genome & annotation，则直接合并。
Dec 6, 2025
Rui Yang

Improve genome annotation using RNA-Seq data

genome annotation
rna-seq
Assemble transcripts:
Dec 4, 2025
Rui Yang

Introduction to CRISPR-Cas9 gene editing system

crispr-cas9
CRISPR-Cas9 is a powerful gene-editing system that enables precise cleavage of double-stranded DNA at specific target sites.
Nov 30, 2025
Rui Yang

CellChat demo

cellchat
demo
For detailed info, see:
Nov 22, 2025
Rui Yang

quality assessment of genome assembly and annotation

genome
annotation
qc
quast
busco
You should first extract the longest transcript of each gene, and then translate them into protein sequences before running BUSCO.
Nov 5, 2025
Rui Yang

Predict CDSs from transcripts de novo

cds prediction
transcript
de novo
td2
For detailed info, see https://github.com/Markusjsommer/TD2.
Nov 4, 2025
Rui Yang

Configure conda

conda
mamba
micromamba
## 1. Install and initialize micromamba
cd /home/yangrui/softs
mkdir micromamba
cd micromamba

wget…
Oct 25, 2025
Rui Yang

Single-cell analysis workflow for adult mouse hippocampus datasets dealed with either human astrocyte or human glioma cells

single-cell omics
human
mouse
hippocampus
astrocyte
glioma
数据需服从正态分布。\(\sigma\) 对异常值很敏感，因此适合于极端严格的场景。
Oct 21, 2025
Rui Yang

Metadata template

metadata
template
metadata_version: v1
Sep 23, 2025
Rui Yang

Misc bioinformatics code

bioinformatics
misc
For detailed info, see https://github.com/ncbi/sra-tools/wiki and https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump.
Sep 21, 2025
Rui Yang

Build reference genome index and align/quantify reads

reference genome index
single-cell omics
scrna-seq
snrna-seq
scatac-seq
Caution: mobivision is not really robust for annotations from non-model organisms (it seems fine for Ensembl annotations). It’s highly recommended that you use cellranger ins…
Sep 20, 2025
Rui Yang

Reference genome and annotation file selection

reference genome
gene annotation
Allele: an allele is one of two or more alternative forms of a DNA sequence at the same locus on homologous chromosomes. This locus may lie within a gene or any other…
Sep 19, 2025
Rui Yang

Foundations and concepts of single-cell omics

single-cell omics
Acceptable/excellent quality metrics:
Sep 18, 2025
Rui Yang

Tree construction

tree construction
For detailed info, see https://iqtree.github.io/ and https://github.com/iqtree/iqtree3.
Jul 9, 2025
Rui Yang

Identify orthologous genes

orthologs
paralogs
orthofinder
For detailed info, see https://orthofinder.github.io/OrthoFinder/ and https://github.com/OrthoFinder/OrthoFinder.
Jul 5, 2025
Rui Yang

Sequence alignments

sequence alignments
Pairwise sequence alignments:
Jul 5, 2025
Rui Yang

Proteomics-related concepts

proteomics
Jun 25, 2025
Rui Yang

Identify EGFP-positive cells via scRNA-Seq

egfp
scrna-seq
mobivision
seurat
trinity
In this doc, we try to identify what cell types those EGFP-positive cells may be via the following steps:
Jun 25, 2025
Rui Yang

Misc NGS concepts

ngs
misc
测序深度：每碱基被测序的平均次数。
Jun 24, 2025
Rui Yang

Concepts of de novo transcriptome assembly

de novo transcriptome assembly
rna-seq
trinity
There are several tools which can be used to perform de novo transcriptome assembly, such as Trinity.
Jun 24, 2025
Rui Yang

Concepts of strand-specific RNA-Seq

rna-seq
strand-specific
Template strand/antisense strand/minus strand: 在转录时，RNA 聚合酶以该链为模板，依据碱基互补配对原则合成 mRNA。简言之，此条链的碱基与 mRNA 的碱基互补配对。
Jun 23, 2025
Rui Yang

Deploy and run RepeatModeler/RepeatMasker

genome masking
repeatmodeler
repeatmasker
# pull the Dfam TETools docker image
# and save it as an SIF image file
singularity pull dfam-tetools-latest.sif docker://dfam/tetools:latest

# clone the Dfam TETools
git…
Jun 17, 2025
Rui Yang

Retrieve high-confidence NDD genes

NDD
gene
Retrieve high-confidence NDD genes from various databases.
Apr 15, 2025
Rui Yang

Bulk RNA-Seq differential expression analysis and batch correction with DESeq2, limma, or sva

bulk rna-seq
differential expression
batch correction
deseq2
limma
sva
Perform batch correction with DESeq2, limma, or sva.
Mar 2, 2025
Rui Yang

Build ENCODE ATAC/ChIP-Seq pipeline indices

encode
atac-seq
chip-seq
index
For more details, refer to ENCODE ATAC-Seq pipeline from GitHub, ENCODE ATAC-Seq pipeline from Google doc, ENCODE ChIP-Seq pipeline from GitHub, and ENCODE ChIP-Seq pipeline…
Feb 28, 2025
Rui Yang

Build ENCODE RNA-Seq pipeline indices

encode
rna-seq
index
For more details, refer to ENCODE RNA-Seq pipeline.
Feb 26, 2025
Rui Yang

DE-related analysis for bulk proteomics

bulk proteomics
differential expression
At present, this pipeline only allows two sample groups contained in your input files.
Jan 16, 2025
Rui Yang

MPRA analysis pipeline

mpra
Before running any of the following steps, you should rename your FASTQ files according to these rules.
Jan 8, 2025
Rui Yang

Misc R code

r
misc
Used to collect various R code snippets.
Jan 2, 2025
Rui Yang

Cut&Tag analysis pipeline

cut&tag
Before running any of the following steps, you should rename your FASTQ files according to these rules.
Dec 30, 2024
Rui Yang

Agilent mRNA microarray analysis using limma

agilent
mrna
microarray
limma
A little example for how to use limma to analyze Agilent mRNA microarray data.
Sep 30, 2024
Rui Yang

Identify housekeeping genes

bulk rna-seq
housekeeping genes
In brief, housekeeping genes are those with higher expression levels, low variances, and ubiquitous expression profiles across samples and species.
Sep 18, 2024
Rui Yang

Bulk RNA-seq pseudotime analysis

bulk rna-seq
pseudotime
In scRNA-seq, various tools, such as Monocle3, provide the capability of performing pseudotime analysis. In brief, assume that there are both progenitors and more…
Sep 9, 2024
Rui Yang
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