SangerBox permanent download address (native messenger tool box)

SangerBox, a new generation of data analysis box, integrates common fool type data analysis software to make analysis easy.

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  • Zhu Rangfei
  • Published at 2017-11-09 16:15
  • Reading (115266)

Do you know how Sanger Zushou's official account queries the immediate impact factors

The magazine impact factor query function of the public account has not been updated for a long time. Recently, it has been revised, mainly in two aspects: 1. The search method has been optimized. Previously, it was necessary to enter a complete magazine name to check the impact factors and partitions. Now it supports fuzzy search, such as searching for p

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  • Zhu Rangfei
  • Issued at 20:00 on November 26, 2019
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R language can be played like this | High quality pictures can be exported like this!

As we all know, visualization is an indispensable part of statistics, and also a very intuitive way to convey information, and the most important thing for SCI article submission is also the processing of images. General magazines require pictures with a minimum resolution of 300 DPI, and some magazines require pictures with a minimum resolution of 6

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  • Easy to count
  • Published at 2017-05-17 14:04
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How to use GEO data for variance analysis

Whether you want to see whether a gene is differentially expressed or to screen the differentially expressed genes in a GEO dataset, this method can definitely help you get twice the result with half the effort First, suppose you have found a set of data GSE32323 This set of data includes 44 samples, of which 17 are matched with

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  • Zhu Rangfei
  • Published on 2017-09-28 10:48
  • Reading (67227)

This should be the simplest and most useful GSEA enrichment analysis tool in history

What is GSEA? Baidu is responsible for this. You should know what GSEA is before using it Then upload the tool screenshot: Generally, we need to prepare three documents for GSEA 1. Expression spectrum of gct format 2. Group Files 3. Rich background files, that is, gmt format

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  • Zhu Rangfei
  • Published on 2017-09-19 10:12
  • Reading (57581)

Use case of GEO chip data converter

Take GEO chip data GSE14520 as an example: First, download GSE14520 data from GEO: It can be seen from the figure that there are 488 samples in total. We select data in the MINIML format (the software only supports this format), and download them: Then we import the file into the software: From Figure

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  • Zhu Rangfei
  • Published on 2017-08-10 10:57
  • Reading (56276)

Abbreviations and full names of 44 cancers specified by TCGA and ICGC

I wonder if you need a Chinese translation. lamlAcute Myeloid LeukemiaaccAdrenocortical carcinomablcaBladder Urothelial CarcinomabocaBone CancerlggBrain Lower Grade GliomabrcaBreast invasive c...

The beautification process of the pheatmap of the heat maps painted in the New Year

In the analysis of gene expression patterns, we often need to visualize multiple gene expression data, so that we can see the gene expression in different samples at a glance. In daily research, we are often used to selecting heat maps to realize the requirement of visualization of this gene expression pattern, and then intuitively express the analysis results of our gene expression pattern.

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  • Zhu Rangfei
  • Published on 2017-06-26 20:57
  • Reading (53301)

Details of SangerBox configuration

The easy-to-use sangerbox is finally online, integrating dozens of gadgets to make scientific research easier

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  • Survey map
  • Published at 18:10, June 12, 2018
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Simple TCGA download tool tutorial

The simple TCGA download tool is a small software that can download TCGA data. It can search available resources online and download them in batches. In addition to downloading, it also provides simple processing of clinical data, converting a single clinical information file in xml format into data in matrix format; In addition, for RNA seq, metaarray, miRNA data also provides the function module of combining single files into matrix format data, and can convert the ENSG_ID in RNA seq to geneSymbol. Here is a tutorial on the use of this software, hoping to help you download TCGA data quickly and in batch.

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  • Fei
  • Published on 2017-03-28 20:11
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NCBI SRA Database Usage Details

As a qualified novice in bioinformatics, how can I do without money for sequencing? I can't help looking for data everywhere To practice basic skills well, you must start with finding data! Today, I will introduce SRA, a database that stores large amounts of high-throughput data. 1. Introduction SRA（Seque...

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  • SXR
  • Published on 2017-03-30 21:40
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Introduction to the usage of UCSCXenaTools package - searching and downloading TCGA, GDC, ICGC and other public database datasets

Download UCSC Xena public dataset

Introduction to FPKM and TPM conversion in TCGA RNAseq data

In the new version of data, TCGA's RNAseq data mainly provides three data downloads, FPKM，FPKM-UQ,Counts， If you want to use edgR and other software to filter differences, you will download and use Counts data, but the author found that TCGA data used edgR and other software to filter differences in the past data analysis

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  • Zhu Rangfei
  • Published on 2017-08-24 10:41
  • Reading (37694)

The case of computing the consistency index in R (Harrell'concordance index: C-index)

C-index， The full English name is concordance index, which is translated into consistency index in Chinese. It was first proposed by Frank E Harrell Jr, professor of biostatistics at Vanderbilt University in 1996. It is mainly used to calculate the differentiation between the predicted value of COX model and the real value in survival analysis, which is similar to the AUC that everyone is familiar with

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  • Zhu Rangfei
  • Published on 2017-06-26 15:32
  • Reading (33707)

R language basic drawing -- line chart

R language basic drawing -- line chart

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  • Shuanger
  • Published on 2017-07-22 15:22
  • Reading (33651)

Take TCGA breast cancer RNA seq data as a WGCNA example

WGCNA (Weighted Correlation Network analysis) is a method of constructing gene co expression networks based on gene expression data. The difference between WGCNA and Differential Gene Analysis (DEG) is that DEG mainly analyzes the difference between samples, while WGCNA mainly analyzes the relationship between genes. WGCNA divides genes into multiple modules by analyzing the relationship between genes. Finally, we can find the molecular characteristics of specific phenotypes through correlation analysis between these modules and sample phenotypes.

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  • Zhu Rangfei
  • Published on 2017-06-04 10:53
  • Reading (32814)

Take the RNA Seq data of TCGA liver cancer as an example of difference analysis

Just wrote an example of how to use GEO data to make differences, such as: https://www.shengxin.ren/article/207 This time, we will use TCGA liver cancer data to demonstrate the following, and we will select the RNA Seq Counts data that you prefer Use TCGA Easy Download Tool to select

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  • Zhu Rangfei
  • Published on 2017-10-26 20:27
  • Reading (31809)

Interpretation of a typical WGCNA article

We identified two modules and 10 hub genes, which are related to tumorigenesis of OSCC. The reference provided by these two modules will promote the understanding of tumorigenesis mechanism in OSCC. In addition, hub genes can be used as biomarkers and therapeutic targets for precise diagnosis and treatment of OSCC in the future.

Teach you to do heat map step by step, from simple to complex

Heat maps are frequently used in molecular biology articles (especially microarray, RNA seq related papers). Heat maps can: 1) Visualize the global expression changes of multiple samples and genes; 2) It shows the clustering relationship of multiple samples or multiple gene expression levels

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  • admin
  • Issued on October 12, 2021-12 16:04
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Take a set of TCGA gastric cancer data to do survival analysis examples in batches

Data preparation 1. To download TCGA RNA Seq data, we use the TCGA simple download tool to download it. Because we are doing prognosis, there is no significant normal sample. As shown in the figure, there are 407 samples in total (this includes all downloadable samples. To download all of them, check the top right corner

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  • Zhu Rangfei
  • Published on 2017-10-28 16:24
  • Reading (31020)

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