Install/Update R and R packages

Posted on 2019-07-17 | In R | | Views:

| 14k | 0:13

Purpose in short: to ease the pain when installing/updating R and R packages. Note: I mainly work under CentOS and Windows environment, so, I am not f ...

Cancer gene collections

Posted on 2019-06-03 | In cancer | | Views:

| 6.2k | 0:06

Reliable cancer gene collections are useful in cancer research. Here I list several such resources. These sets can be devided into two categories: mut ...

ATAC-seq data analysis: from FASTQ to peaks

Posted on 2019-03-20 | In Peak , ATAC-seq | | Views:

| 29k | 0:26

The content were compiled from multiple resources on the internet (forum, papers, workshop etc.). I could not indicate all the sources, but I want to ...

Calculate FRiP score

Posted on 2019-03-20 | In Peak , QC | | Views:

| 7.8k | 0:07

Ref: ENCODE - Terms and Definitions Fraction of reads in peaks (FRiP) - Fraction of all mapped reads that fall into the called peak regions, i.e. usa ...

Understand Bioconductor Annotation Packages

Posted on 2018-09-18 | In R , Bioconductor | | Views:

| 22k | 0:20

This note is to help me figure out the design schema of annotation packages in Bioconductor. And this note is mainly compiled from: Annotation Packag ...

Biological ID Conversion

Posted on 2018-09-18 | In bioinformatics , basic | | Views:

| 16k | 0:14

ID mapping is annoying but we have to face very often. This note is a collection of methods to deal with this trouble. R (Bioconductor) There are lot ...

Remove Microbial Contamination in Reads

Posted on 2018-07-25 | In reads , contamination | | Views:

| 32k | 0:29

Purpose in short: I’ve got both illumina (PE and MPE) and PacBio reads of an insect for de novo geome assembly. Since whole bodies were used for DNA e ...

Genome Assembly Pipeline: wtdbg

Posted on 2018-06-30 | In genome assembly , TGS pipeline | | Views:

| 7.7k | 0:07

Introduction wtdbg has two git repos: wtdbg and wtdbg-1.2.8, and the author Jue Ruan (who also developed SMARTdenovo) introduces them as: wtdbg: A f ...

Detect Microbial Contamination in Contigs by Kraken

Posted on 2018-06-28 | In genome assembly , contamination | | Views:

| 11k | 0:10

Purpose in short: I want to detect (and remove) potential contaminants in the genome assembly, and Kraken is a tool designed for that. Introduction F ...

Viral Expression in RNA-seq data

Posted on 2018-05-04 | In RNA-seq , viral expression | | Views:

| 3.9k | 0:04

Recently I wanted to check viral expression from RNA-seq data. I found two good examples: Cao S, Strong MJ, Wang X, Moss WN, Concha M, Lin Z, O’Grady ...