Bioinformatics-Department-C-BIG mofa_tutorial issues

Bioinformatics-Department-C-BIG / mofa_tutorial

0 stars 0 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Predict missing proteomics

#43 eathieniti opened 1 week ago
1
Impute MOFA missing omics for all time points to allow running of further multi omics tools

#42 eathieniti opened 1 week ago
0
Rerun MOFA by including also genetic cohort patients

#41 eathieniti opened 1 month ago
0
Redo the intersection of pathways by reading from the ones in pcgse!

#40 eathieniti opened 1 month ago
0
Unique processes in factors - unique that do not exist in run with controls only

#39 eathieniti opened 1 month ago
1
PPI networks over time for the CSf PROTEINS

#38 eathieniti opened 3 months ago
0
Investigate: Why are the expressions of some pathways negative in baseline and then poisitive?

#37 eathieniti opened 3 months ago
2
Estimation of the proportions of NK cells using more specific markers - CD57 etc

#36 eathieniti opened 3 months ago
0
untargeted proteomics DE-same script as the targeted

#35 eathieniti opened 3 months ago
0
Temporal changes of pathways per cluster

#34 eathieniti opened 4 months ago
1
Enrichment analysis for proteins per cluster

#33 eathieniti opened 4 months ago
0
Cluster characterization - Unique mechanisms in clusters

#32 eathieniti opened 4 months ago
3
Heatmaps proteins and RNAs with top factor features and cluster labels to understand differences between them

#31 eathieniti opened 4 months ago
0
MOFA characterization of factors, top scores, cell types, pathways, molecules

#30 eathieniti opened 5 months ago
0
Pathway analysis PCGSE - PLOT

#29 eathieniti opened 5 months ago
0
Run epigenomics analysis from PPMI

#28 eathieniti opened 5 months ago
0
Literature review: Immune system cells in Parkinsosns

#27 eathieniti closed 1 month ago
0
Plot cell type proportions over time for different groups : disease control genetic

#26 eathieniti opened 5 months ago
0
Does removing factor 2 reduce the ncRNA findings..?

#25 eathieniti opened 5 months ago
1
Estimate cell type compositions from the RNAseq and mirna seq datasets

#24 eathieniti opened 5 months ago
7
Multi-omics signatures over time

#23 eathieniti opened 5 months ago
1
Compare MOFA run and NP2PTOT clusters using V08 run only and all visits run

#22 eathieniti opened 6 months ago
1
MOFA group run

#21 eathieniti opened 6 months ago
2
TIMEOMICS by cluster and all toghether

#20 eathieniti opened 6 months ago
3
Obtain the temporal changes of the signature- how does it vary over time?? consider timeomics

#19 eathieniti opened 6 months ago
1
Add snps and genetic subtypes

#18 eathieniti opened 6 months ago
0
Analyse DNA METHYLATION

#17 eathieniti closed 1 month ago
0
New mofa run clustering after cell type composition correction (NP2PTOT + MOCA)

#16 eathieniti closed 4 months ago
11
DEseq analysis with and without correction for cell composition and overlap with significant genes from rnaseq portal

#15 eathieniti opened 6 months ago
5
Correction of RNA sequencing data with cell composition - comparisons

#14 eathieniti opened 6 months ago
2
Factor analysis: Annotations of factors and enrichment analysis

#13 eathieniti opened 7 months ago
0
Mir-gene-tf-gene network signatures

#12 eathieniti opened 7 months ago
6
STRINGdb interactions

#11 eathieniti opened 7 months ago
0
Differences in DE pathways between clusters for all time points

#10 eathieniti opened 7 months ago
2
Cluster comparisons - mechanisms + prior knowledge networks

#9 eathieniti opened 7 months ago
3
mir to genes co expression

#8 eathieniti opened 7 months ago
0
rrvgo analysis to group GO terms from mofa runs

#7 eathieniti opened 7 months ago
1
Plot clinical trajectories per cluster-- create function and run from the cluster analysis

#6 eathieniti opened 7 months ago
1
Assess correlations and effect with neutrophils and lymphocytes

#5 eathieniti opened 7 months ago
3
New subgroups results after batch correction for each of the scales

#4 eathieniti opened 7 months ago
6
Rerun MOFA cluster analysis and enrichment and annotation of factors

#3 eathieniti opened 7 months ago
0
Remove Batch effects from RNA sequencing and rerun mofa

#2 eathieniti closed 5 months ago
5
Add function to run enrichment plots from a PGCSE

#1 eathieniti opened 7 months ago
0