Bioinformatics (KF)
Lecturer
Hubert Hackl
Schedule
| Day | Date | Room | Time |
| Tuesday | 09.12.2025 | PC03 FP301180 | 09:00-12:00 |
| Tuesday | 09.12.2025 | PC03 FP301180 | 13:00-16:00 |
| Wednesday | 10.12.2025 | PC04 FP301160 | 09:00-12:00 |
| Wednesday | 10.12.2025 | PC01 FP301200 | 13:00-16:00 |
| Thursday | 11.12.2025 | PC03 FP301180 | 09:00-12:00 |
| Thursday | 11.12.2025 | PC03 FP301180 | 13:00-16:00 |
| Friday | 12.12.2025 | PC03 FP301180 | 09:00-12:00 |
Notes
Content
| 1 | Predictive methods on protein sequences (Protein domains, Signal P, NetMHCPan) |
| 2 | Sequence alignment and databases (BLAST, NCBI, TCGA, Firebrowse, TCIA, GEO, IntOgen, cBioPortal) |
| 3 | Differentially expressed genes (microarrays/proteomics, RNAseq) (R/Bioconductor, limma, DEseq2) |
| 4 | Expression profiling and clustering (Genesis, Heatmaps) |
| 5 | Gene ontology, Pathway analysis (DAVID, KEGG, Reactome, ConsensusPathDB, ClueGO, Enrichr) |
| 6 | Network analysis (Cytoscape, STRING) |
| 7 | Gene set enrichment analysis (GSEA, Deconvolution) |
| 8 | Predictive and prognostic marker (signatures) (logistic regression, survival analysis) |
| 9 | Single cell RNAseq visualizations (t-SNE, UMAP) |
Data and scripts
EXPR_GSE67501.txt
get_deg.R
deg_GSE67501.txt
COUNT_MATRIX_GENE.txt
TARGET_HEL.txt
get_deg_HEL.R
DEG_HEL14D_HELCTRL.txt
LUAD.txt
LUAD_MATRIX_TN_COUNTS.txt
LUAD_MATRIX_TN_TPM.txt
LUAD_MATRIX_PRIM_TPM.txt
LUAD_CLIN.txt
get_matrix_tn_rawcounts.R
get_matrix_tn_TPM.R
get_matrix_prim_TPM.R
deseq2_tn.R
results_tn.txt
LUAD_IMMUNE.txt
RELAPSE.rnk
gensets.gmx
CACO2_OXO_DEG.rnk
GENESETS.gmt
GSEA.R
CRC_PRIM_LOG2TPM1_2.txt
GSVA.R
GSVA_CRC.txt
CRC_PRIM_TPM_2.txt
deconv.R
BOXPLOT.R
OS.R
OS2.R
GSE51373_RAW.tar
target.txt
get_eset.R
normalized_data.txt
get_deg_S_R.R
deg_S_R_GSE51373.txt
deg_S_R_GSE51373_UNIQUE.txt
ROC.R
SCRNASEQ.R
matrix.mtx
genes.tsv
barcodes.tsv
Databases and links
cBioPortal
intOgen
TCGA
Genomic Data Commons Data Portal
ICGC data portal
Firebrowse
TCGAbiolinks
The Cancer Immunome Atlas (TCIA)
Variant Effect Predictor
netMHCpan 4.2 server
GSEA
DAVID
ConsensusPathDB
Enrichr
KEGG
Reactome
Genesis
Cytoscape
GEO
BLAST
Gene
SignalP
Bioconductor
R_Bioconducter Manuals UC Riverside
Next-Generation Sequencing Analysis Resources
Statistical Genomics Analysis
Introduction to Single_Cell RNA-seq
Single-cell best practices
Example of RNAseq preprocessing
STHDA R plots (e.g. ggplot2/ggpubr)
R commands
R for dummies
R for Biologists
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