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DMSO
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MAYBE TODO for paper: Multimodal models
#17
annashcherbina
closed
6 years ago
1
TODO for paper #7: Flesh out the vignette on H3K27me3 marks disappearing with DMSO treatment, corresponding to increased binding of pioneer motifs (Figure 4 ? )
#16
annashcherbina
opened
6 years ago
0
TODO for paper #6: Jingling asked for exon coordinates for PI3K & Downstream genes for her validation approach (Figure 3 should be the validation results on PI3K and eventually other genes)
#15
annashcherbina
opened
6 years ago
1
TODO for paper #5: Update CIRCOS plot to focus on individual pathways (Figure 2)
#14
annashcherbina
opened
6 years ago
0
TODO for paper #4 : Re-train top-performing model with ENCODE weight inits
#13
annashcherbina
opened
6 years ago
3
TODO for paper #3 Main summary figure (i.e. Figure 1)
#12
annashcherbina
opened
6 years ago
2
TODO for paper #2: DPGP clustering analysis
#11
annashcherbina
opened
6 years ago
9
TODO for paper #1: Chromatin state distribution plot by cell cycle phase & treatment status
#10
annashcherbina
opened
6 years ago
6
Analysis of TAD enrichment for differential ATAC peaks and genes
#9
annashcherbina
opened
6 years ago
0
CTCF motif scan & overlap with known chromatin loops
#8
annashcherbina
opened
6 years ago
0
kmeans clustering of gene expression
#7
annashcherbina
opened
7 years ago
5
PCA analysis of RNA-seq data
#6
annashcherbina
opened
7 years ago
2
rlogTransform(counts) without sva versus asinh(tpm)-SVA
#5
annashcherbina
opened
7 years ago
0
Surrogate variable analysis for top 2 candidate models
#4
annashcherbina
opened
7 years ago
4
Venn Diagram of Differential Genes for the 12 Model Approaches
#3
annashcherbina
opened
7 years ago
0
Model Comparison -- Total differential genes by task
#2
annashcherbina
opened
7 years ago
0
RNA-seq voom mean-variance trend
#1
annashcherbina
opened
7 years ago
0