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YeoLab
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skipper
Skip the peaks and expose RNA-binding in CLIP data
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Questions about the peak output columns in reproducible_enriched_windows directory
#40
zhenyu7500
opened
3 days ago
1
Handling Consecutive Enriched Windows as Merged Peaks
#39
VandaLovejoy
opened
3 days ago
1
Why are flank and shift used in this analysis pipeline?
#38
VandaLovejoy
closed
3 days ago
2
RBP bound sequence in repetitive elements (rRNA)
#37
ychy1
closed
1 week ago
2
RE: Issue with running skipper in mamba/conda environment
#36
TimothyTse001
opened
2 weeks ago
1
Hi Brian, please test my code on skipper + ML + genetics stuffs
#35
algaebrown
closed
5 days ago
22
significant difference in read depth between the IP and input data， but some peaks missed
#34
zhenyu7500
closed
2 weeks ago
4
How do I modify skipper_config.py to re-run snakmake with the bam generated earlier in your script
#33
zhenyu7500
closed
1 month ago
1
adds a second round of trimming to remove adapter dimers
#32
byee4
closed
1 month ago
0
information about intergenic enriched windows
#31
VandaLovejoy
closed
2 months ago
2
Resources
#30
byee4
closed
6 months ago
0
Container testing
#29
byee4
closed
6 months ago
0
Use sortBed instead of unix sort
#28
NaotoKubota
opened
8 months ago
0
Some misleading in Skipper_config.py
#27
Lindky
closed
8 months ago
2
Merge edit-testing branch to main branch. Intend to simplify setup process and add example dataset.
#26
howardxu520
closed
8 months ago
0
Error in rule get_nt_coverage:
#25
byee4
closed
8 months ago
4
question about enriched terms
#24
yos-hida
closed
9 months ago
2
update memory resources
#23
byee4
closed
8 months ago
0
Merge main changes to README into WIP
#22
byee4
closed
10 months ago
0
update memory sys reqs and comment non-working modules
#21
byee4
closed
8 months ago
0
Question about Tested windows.
#20
FionaMoon
closed
10 months ago
4
Modulize skipper
#19
algaebrown
closed
10 months ago
4
How to filter the output of skipper?
#18
FionaMoon
closed
4 months ago
7
analysis with only 1 SMI sample available
#17
MSajek
closed
1 year ago
2
[minor] Inconsistent output format between enriched_windows and enriched_re
#16
algaebrown
closed
1 year ago
1
Paired-end sequencing in Skipper Manifest
#15
yvazirabad
closed
1 year ago
4
NameError in line 134 of Skipper.py: name 'directory' is not defined File "Skipper.py", line 134, in <module>
#14
MSajek
opened
1 year ago
6
Execution halted in fit_clip_betabinom.R
#13
byee4
closed
1 year ago
3
missing value where TRUE/FALSE needed in finemap_enriched_windows.R
#12
byee4
opened
1 year ago
0
How to understand parameter INFORMATIVE_READ?
#11
FionaMoon
closed
1 year ago
5
merges updated rule reqs
#10
byee4
closed
1 year ago
0
Execution haulted due to error in rule fit_input_betabinomial_re_model
#9
ajritter8
closed
1 year ago
11
Errors when empty reproducible windows file is used as input to consult_term_reference.R
#8
byee4
closed
4 months ago
1
finemapped_windows from the manuscript
#7
CharlotteAnne
closed
1 year ago
3
R scripts appear incompatible with some R packages
#6
byee4
closed
1 year ago
2
(partition_bam_reads) Error: line number 29869383 of file - has 3 fields, but 6 were expected.
#5
byee4
opened
1 year ago
3
STAR alignment fails for larger (~80M) datasets due to limitOutSJcollapsed
#4
byee4
closed
1 year ago
1
Where can I find "gencode.v38.annotation.k562_totalrna.gt1.tiled_partition.features.tsv.gz" ?
#3
byee4
closed
2 years ago
1
Error in step findMotifsGenome.pl
#2
byee4
closed
1 year ago
2
Error in call_enriched_windows.R
#1
byee4
closed
1 year ago
2