Appendix IV. Teaching Materials

1) Teaching Lecture PPTs

2) Teaching Docker

Download Link for Docer images

  • PART I + II + PART III.1-3

    • docker image name: bioinfo_PartI-PartII-PartIII1-3.tar.gz

    • software installed: BLAST 2.6.0+; bowtie 1.0.0; samtools 1.7 (using htslib 1.7-2); TopHat v2.0.9; cufflinks v2.1.1; cuffmerge v2.1.1; cuffdiff v2.1.1; R 3.5.1; perl v5.26.1; Python 2.7; bamtools 1.0.2; java 1.8.0_181; rMATS-turbo-Linux-UCS4 v3.1.0; homer v4.10.3;

  • PART III.1 Paired-end mapping

    • docker image name: bioinfo_pairend.tar.gz

    • software installed: STAR:2.5.3a;

  • PART III.4. Network coexpression 1

    • docker image name: bioinfo-coexp.tar.gz

    • software installed: R 3.5.1 ; bedtools v2.27.1

  • PART III.4. Network coexpression 2

    • docker image name: bioinfo_mirna_target.tar.gz

    • software installed: miRanda;psRobot: v1.2; miRanda: aug2010;

  • PART III.5. Motif

    • docker image name: bioinfo_motif.tar.gz

    • software installed: R 3.5.1; meme 4.11.4; RNAfold 2.4.8; BEAM; RNApromo

  • PART III.6. RNA Regulation Analysis 1

    • docker image name: bioinfo_rnaeditor.tar.gz

    • software installed: RNAEditor

  • PART III.6. RNA Regulation Analysis 2

    • docker image name: bioinfo_tsinghua_6.2_apa_6.3_ribo_6.4_structure.tar.gz

    • software installed: perl v5.26.1; DaPars; Ribowave; R 3.5.1; bedtools v2.25.0; shapemapper

  • PART III.6. RNA Regulation Analysis 3

    • docker image name: bioinfo.chimeric.tar.gz

    • software installed: STAR-Fusion: 1.8.1;

  • PART III.6. RNA Regulation Analysis 4

    • docker image name: bioinfo_snv.tar.gz

    • software installed: STAR: 2.7.1a; annovar:2018-04-16; GATK:4.1.3.0;

  • PART III.7. Clinical Analysis 1

    • docker image name: bioinfo_roc_survival.tar.gz

    • software installed: R 3.5.1; Python 2.7

  • PART III.7. Clinical Analysis 2

    • docker image name: bioinfo_pca_machine.tar.gz

    • software installed: Anaconda 2019.10

  • PART IV.2-3. Machine learning

    • docker image name: bioinfo_pca_machine.tar.gz

    • software installed: Anaconda 2019.10

3) Teaching Videos

Content

Youtube

Bilibili

How to use docker

@Youtube

@Bilibili

Linux (视频配套文档)

@Youtube

@Bilibili

Vim

@Youtube

@Bilibili

R

@Youtube

@Bilibili

Genome Browser: IGV

@Youtube

@Bilibili

Genome Browser: UCSC

@Youtube

@Bilibili