BiocenterInnsbruck Medical University
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BIOINFORMATICS (KF)
VU041035 WS2024|25



LECTURER

Hubert Hackl 


SCHEDULE

DayDateRoomTime
Mon9.12.2023FP3 C109:00-12:00, 13:00-16:00
Tue10.12.2023FP3 C109:00-13:00, 14:30-16:30
Wed11.12.2023FP3 C409:00-12:00
Wed11.12.2023FP3 C313:00-16:00
Thu12.12.2023FP3 C409:00-12:00


CONTENT

I. Predictive methods on protein sequences (Protein domains, Signal P, NetMHCPan)
II. Sequence alignment and databases (BLAST, NCBI, TCGA, Firebrowse, TCIA, GEO, IntOgen, cBioPortal)
III. Differentially expressed genes (microarrays, RNAseq) (R/Bioconductor, limma, DEseq2)
IV. Expression profiling and clustering (Genesis, Heatmaps)
V. Gene ontology, Pathway analysis (DAVID, KEGG, Reactome, ConsensusPathDB, ClueGO, Enrichr)
VI. Network analysis (Cytoscape, STRING)
VII. Gene set enrichment analysis (GSEA, Deconvolution)
VIII. Predictive and prognostic marker (signatures) (logistic regression, survival analysis)
IX. Single cell RNAseq visualizations (t-SNE, UMAP)


NOTES

Notes [pdf]
Computational Exercises [pdf]


DATA AND SCRIPTS

EXPR_GSE67501.txt [txt]
get_deg.R [R]
deg_GSE67501.txt [txt]
COUNT_MATRIX_GENE.txt [txt]
TARGET_HEL.txt [txt]
get_deg_HEL.R [R]
DEG_HEL14D_HELCTRL.txt [txt]
LUAD.txt [txt]
LUAD_MATRIX_TN_COUNTS.txt [txt]
LUAD_MATRIX_TN_TPM.txt [txt]
LUAD_MATRIX_PRIM_TPM.txt [txt]
LUAD_CLIN.txt [txt]
get_matrix_tn_rawcounts.R [R]
get_matrix_tn_TPM.R [R]
get_matrix_prim_TPM.R [R]
deseq2_tn.R [R]
results_tn.txt [txt]
LUAD_IMMUNE.txt [txt]
RELAPSE.rnk [rnk]
gensets.gmx [gmx]
CACO2_OXO_DEG.rnk [rnk]
GENESETS.gmt [gmt]
GSEA.R [R]
CRC_PRIM_LOG2TPM1_2.txt [txt]
GSVA.R [R]
GSVA_CRC.txt [txt]
CRC_PRIM_TPM_2.txt []
deconv.R [R]
BOXPLOT.R [R]
OS.R [R]
GSE51373_RAW.tar [tar]
target.txt[txt]
get_eset.R [R]
normalized_data.txt [txt]
get_deg_S_R.R[R]
deg_S_R_GSE51373.txt [txt]
deg_S_R_GSE51373_UNIQUE.txt [txt]
ROC.R [R]
SCRNASEQ.R [R]
matrix.mtx[mtx]
genes.tsv [tsv]
barcodes.tsv [tsv]


DATABASES/TOOLS AND LINKS

cBioPortal
intOgen
TCGA
Genomic Data Commons Data Portal
ICGC data portal
Firebrowse
The Cancer Immunome Atlas (TCIA)
Variant Effect Predictor
netMHCpan 4.0 server
GSEA
DAVID
ConsensusPathDB
Enrichr
KEGG
Reactome
Genesis
Cytoscape
GEO
BLAST
Gene
SignalP
Bioconductor
R_Bioconducter Manuals UC Riverside
Next-Generation Sequencing Analysis Resources
Introduction to Single_Cell RNA-seq
Example of RNAseq preprocessing
STHDA R plots (e.g. ggplot2/ggpubr)
R commands
R for dummies
Services
Research
Education
Setting