Description Hi-C technology is a high-throughput sequencing technique used to capture three-dimensional structural information of chromatin across the entire genome. Through this technology, we can study the spatial organization of chromatin within the cell nucleus, such as chromatin compartments, topologically associated domains (TADs), and chromatin loops. These structures play important roles in key life activities … Read more
Introduction Since 2021, Biomamba’s bioinformatics base has been producing many tutorials on single-cell sequencing, which have garnered a significant number of views. While creating these tutorials, we realized that the data from single-cell sequencing is generally very large, making it difficult for individuals to process such big data on their personal computers. Therefore, it is … Read more
Introduction Starting today, we will officially begin our Linux learning journey in the command line. To provide better tutorials, I have purchased and reviewed several books, and I will mainly refer to the book below for explanations. If you feel that my updates are slow, you can also take a look at the book yourself; … Read more
Introduction In the previous lesson, we provided a detailed introduction to the various components of computer hardware and their basic operating methods (following Biomamba to learn Linux | 1. Computer Hardware Composition), but if a computer only has hardware, it is merely a shell without a soul. Only when software is installed can this pile … Read more
1. Quality Control of Raw Data The processing of raw data in single-cell sequencing converts the FASTQ files output from sequencers into a more analyzable format, such as a count matrix. This count matrix represents the estimated unique molecular counts for each gene in each quantified cell, sometimes categorized based on the inferred splicing status … Read more
Database Introduction MSigDB (Molecular Signatures Database) is a widely used gene set database developed and maintained by the Broad Institute. MSigDB contains several carefully curated collections of gene sets, primarily divided into the following categories: Hallmark Gene Sets 50 selected, well-defined biological states and processes Reduces redundancy and overlap, providing clearer analytical results Positional Gene … Read more
What is conda? It is similar to an app store for mobile phones, where you can download the necessary software. There are three versions: conda, miniconda, and anaconda. Here, we will use miniconda as an example based on our needs. unsetunset1. Downloading and Installing condaunsetunset Link to download the conda mirror: https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/ After selecting the … Read more
Why Use the Linux System In my opinion, the Linux operating system and its command line interface are the most suitable for bioinformatics analysis. There are three main reasons: Long-term stability Most software is only available in Linux versions The powerful Bash commands simplify tedious tasks, especially repetitive work However, for beginners, getting accustomed to … Read more
Click the blue text above to follow us immediately When children express a desire to learn programming, Python and graphical programming (Scratch or Kitten) may be the first choices. However, today we will discuss a seemingly “hardcore” yet immensely promising option—C++. It is not only the “key to success” in informatics competitions but also the … Read more
Recently, several teachers shared some resources for learning Python on WeChat. Compared to R, Python is a true programming language that can be used not only for scripting and numerical calculations but also for writing command-line programs, developing user interface applications, creating websites, plotting, and calling functions from libraries written in C, C++, and Fortran, … Read more