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bcbio
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bcbioR
R package with well defined templates for most common pipelines
https://bcbio.github.io/bcbioR/
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Options for GRN with single cell
#49
lpantano
opened
2 days ago
0
sc normalization and clustering
#48
lpantano
opened
2 weeks ago
0
sc DE discussion
#47
lpantano
opened
2 weeks ago
0
Chipseq qc
#46
lpantano
closed
1 week ago
2
DEseq report discussion
#45
lpantano
opened
2 weeks ago
0
rough draft of methylation template
#44
lpantano
closed
2 weeks ago
0
cutandrun report elements
#43
abartlett004
opened
1 month ago
3
Upgrade to usethis functions
#42
lpantano
opened
1 month ago
0
DEG rdata annotation assumes human reference
#41
epartan
opened
1 month ago
1
avoid samples with `-` or other character is not `_alphanumeric`
#40
lpantano
closed
3 weeks ago
1
Extending de templates
#39
lpantano
closed
1 month ago
0
Hot fix release
#38
lpantano
closed
2 months ago
0
Support comparing multiple DESeq2 results
#37
lpantano
opened
2 months ago
0
Support multiple contrasts in the same report
#36
lpantano
opened
2 months ago
0
add checks for low count genes?
#35
eberdan
opened
2 months ago
0
potentially use this package for more palette options
#34
lpantano
opened
2 months ago
0
more hot fixes for demo
#33
lpantano
closed
2 months ago
0
readme tweaks
#32
abartlett004
closed
2 months ago
0
demo ready fixes
#31
lpantano
closed
2 months ago
0
0.2.1
#30
lpantano
closed
3 months ago
0
make sanitize_datatable into package function
#29
abartlett004
opened
3 months ago
0
Feedback in development branch
#28
lpantano
opened
3 months ago
1
check samplesheet function to ensure files exist
#27
abartlett004
opened
3 months ago
0
Update README.md
#26
eberdan
closed
3 months ago
0
Update QC_nf-core.Rmd
#25
eberdan
closed
3 months ago
0
Update params_qc_nf-core.R
#24
eberdan
closed
3 months ago
0
Release 0.1.2
#23
lpantano
closed
3 months ago
0
Fix code with real nfcore/rnaseq projects
#22
lpantano
closed
4 months ago
0
include emma's file
#21
abartlett004
closed
4 months ago
0
introduce changes from Emma
#20
lpantano
opened
4 months ago
0
Updated common repository of gene sets (hallmark, reactome, etc).
#19
lpantano
opened
4 months ago
0
Common repository for lists of protein coding genes
#18
lpantano
opened
4 months ago
0
Common repository (dropbox?) for annotations to add to DE lists
#17
lpantano
opened
4 months ago
0
metrics excluded from nfcore
#16
abartlett004
closed
2 months ago
0
Adapt DE report to nf-core
#15
lpantano
closed
2 months ago
0
v0.1.1
#14
lpantano
closed
4 months ago
0
similar projects
#13
lpantano
opened
4 months ago
0
Interactive volcano plot with glXYPlot
#12
upendrabhattarai
opened
4 months ago
0
Enrichment analysis flexibility
#11
lpantano
opened
4 months ago
0
Options for batch effect in data
#10
lpantano
closed
2 months ago
0
RUVSeq to be optional
#9
lpantano
closed
4 months ago
0
DE - coefficient vs contrasts
#8
lpantano
opened
4 months ago
0
DE_template_example.Rmd - subset discussion
#7
lpantano
opened
4 months ago
0
Viridis for Heatmap
#6
lpantano
closed
2 months ago
0
QC metrics labels to default size be larger
#5
lpantano
closed
2 months ago
0
PCA
#4
lpantano
closed
2 months ago
0
get sc script from Noor
#3
lpantano
opened
4 months ago
0
heatmap with genes and samples
#2
lpantano
closed
2 months ago
0
gene plot with dots
#1
lpantano
closed
4 months ago
0