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afrendeiro
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pipelines
[deprecated] Pipelines for ngs
GNU General Public License v2.0
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Use sample.trimmed2 in Quant-seq pipeline
#31
adelq
opened
7 years ago
0
Implemented oop-based project management and pipeline
#30
afrendeiro
closed
9 years ago
0
Add average and standard deviation of library size from PE experiments to annotation sheet
#29
afrendeiro
opened
9 years ago
0
Don't require annotation sheet as argument - look for it, fail if not found
#28
afrendeiro
opened
9 years ago
0
Implement NSC and RSC
#27
afrendeiro
closed
9 years ago
1
Implement FRiP
#26
afrendeiro
opened
9 years ago
1
Add path of control sample bam to annotation sheet
#25
afrendeiro
closed
9 years ago
0
Implement no overwrite by default
#24
afrendeiro
closed
9 years ago
1
Merged replicates contain redundant samples
#23
afrendeiro
closed
9 years ago
0
Optimize peak calling dependent on technique
#22
afrendeiro
opened
9 years ago
0
updated chromosome lengths index
#21
afrendeiro
closed
9 years ago
0
Generate table of sample statistics
#20
afrendeiro
closed
9 years ago
1
Remove duplicate tsss
#19
afrendeiro
closed
9 years ago
0
Implement IDR
#18
afrendeiro
opened
9 years ago
0
Support pair-end input
#17
afrendeiro
closed
9 years ago
0
Pair ip with input by sample name, not index
#16
afrendeiro
closed
9 years ago
0
Reads on tracks are not extended to average fragment length
#15
afrendeiro
closed
9 years ago
0
Better UCSC track display
#14
afrendeiro
closed
9 years ago
0
Plots of enrichment around TSSs
#13
afrendeiro
closed
9 years ago
0
Complete list of requirements in README
#12
afrendeiro
opened
9 years ago
0
More checks on annotation sheets
#11
afrendeiro
closed
9 years ago
1
Different motif finding settings for different factors
#10
afrendeiro
closed
9 years ago
0
Differential peak calling between conditions/cell lines
#9
afrendeiro
closed
9 years ago
0
Specific processing of broad histone marks
#8
afrendeiro
closed
9 years ago
0
ATAC-seq specific pipeline
#7
afrendeiro
closed
9 years ago
2
Automatic IP/input detection and pairing
#6
afrendeiro
closed
9 years ago
1
Assert tagmentation-specific processing of sample from technique (e.g. DNase, ATAC-seq)
#5
afrendeiro
closed
9 years ago
0
ucsc track description should include nature of track (full reads, 5prime)
#4
afrendeiro
closed
9 years ago
1
Separate track hubs for each genome in the sample annotation sheet
#3
afrendeiro
closed
9 years ago
1
Log wont track successful exit
#2
afrendeiro
closed
9 years ago
0
expose tracks to outside
#1
afrendeiro
closed
9 years ago
0