hputnam Meth_Compare issues

hputnam / Meth_Compare

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SF3.png to SF3.jpg

#110 jpuritz closed 3 years ago
0
Are we happy with the Results?

#109 shellywanamaker closed 3 years ago
0
Plot Mcap and Pact Circos Manuscript and Supp Figures

#108 hputnam closed 3 years ago
0
Decide on target journal

#107 shellywanamaker closed 3 years ago
0
Double check experimental set up is clear in methods

#106 shellywanamaker closed 3 years ago
0
Add number of loci to PCA plots

#105 shellywanamaker closed 3 years ago
0
update main text to include new thresholded PCA results

#104 shellywanamaker closed 3 years ago
0
Add thresholded PCAs to main text

#103 shellywanamaker closed 3 years ago
1
Reduce excessive numbers in results text

#102 shellywanamaker closed 3 years ago
0
Fig. 2a and c: add zoomed in plots for 5x and 10x cov

#101 shellywanamaker closed 3 years ago
1
standardize estimated fraction of genome-wide CpGs to genome size (SUPP FIG 3)

#100 shellywanamaker closed 3 years ago
0
Check coverage of 5x, 10x, 50x and 100x for common loci comparisons to address Katie's question

#99 mgavery closed 3 years ago
18
histograms of percent methylation for CpGs that overlap between methods

#98 shellywanamaker closed 3 years ago
19
Finalize NCBI submission of raw sequence data

#97 hputnam closed 3 years ago
3
Conform to MEE journal formatting requirements

#96 shellywanamaker closed 3 years ago
0
generate README map in code folder of all numerical file names

#95 hputnam closed 3 years ago
2
Add in C1 mapping information to methods and alignment results

#94 hputnam closed 4 years ago
0
confirm ANOVAs for BS conversion efficiency

#93 shellywanamaker closed 4 years ago
0
Identify location of Lambda conversion and remove xls file when code is posted

#92 hputnam closed 4 years ago
3
Organize README.md files in repo

#91 yaaminiv closed 3 years ago
2
Recharacterize locations for DMC

#90 yaaminiv closed 4 years ago
2
Review abstract

#89 shellywanamaker closed 4 years ago
1
Fix PCA plots in supp material

#88 shellywanamaker closed 4 years ago
0
Confirm # of common 5x CpG loci

#87 shellywanamaker closed 4 years ago
1
Median methylation by gene for each sample

#86 yaaminiv closed 4 years ago
1
Plot to examine grouping of triplicate CpG patterns by method

#85 hputnam closed 4 years ago
1
Check Mcap genomic location stacked barplot

#84 yaaminiv closed 4 years ago
1
Identify Orthologous gene set between Species for comparison

#83 hputnam closed 4 years ago
1
plot histograms of # of CpG per gene for both species in all 3 methods

#82 hputnam closed 4 years ago
0
Standardize the use of MBDBS across all figures

#81 hputnam closed 4 years ago
1
Normalization of counts to gene length and relative frequency

#80 hputnam closed 4 years ago
1
Normalization of gene number and gene set for figure 6

#79 hputnam closed 4 years ago
0
standardize the order of reporting species

#78 hputnam closed 4 years ago
0
Add upset plot and coverage analysis methods to manuscript

#77 shellywanamaker closed 4 years ago
1
plot gene presence absence by method and gene expression levels of genes found in each method

#76 hputnam closed 4 years ago
0
Check gene.gff has 63227 genes

#75 hputnam closed 4 years ago
3
Choose color palette and 3 specific colors for methods and standardize across graphics

#74 hputnam closed 4 years ago
3
Need all gene CpG intersection information to link to expression and GO

#73 hputnam closed 4 years ago
5
Revise stacked barplots

#72 yaaminiv closed 4 years ago
2
Pull gene sequence and protein sequence from Pact Structural_annotation_abintio.gff

#71 hputnam closed 4 years ago
7
Update scripts + README

#70 yaaminiv closed 4 years ago
4
Functional Annotation of Mcap and Pact gene sets

#69 hputnam closed 4 years ago
13
Figure out statistical method to compare CpGs in various categories

#68 yaaminiv closed 3 years ago
15
Create analogous figure to Liew Fig 1B for CDS/intron data

#67 yaaminiv closed 4 years ago
1
Revise CpG methylation status stacked barplots

#66 yaaminiv closed 4 years ago
1
Separate upstream and downstream flanks

#65 yaaminiv closed 4 years ago
1
New union bedgraphs with read count data

#64 yaaminiv closed 4 years ago
4
Create bed files of MBD v WGBS and RRBS DMC for genome feature annotation

#63 mgavery closed 4 years ago
5
create UpSet plot

#62 shellywanamaker closed 4 years ago
4
Create bed files of different method-associated loci coverage

#61 sr320 closed 4 years ago
3