jernst98 ChromHMM issues

jernst98 / ChromHMM

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issues

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NeighborhoodEnrichment error

#60 katsikora closed 1 month ago
2
On this data the INFORMATION initialization strategy can only support 4 states

#59 LHXqwq closed 3 days ago
9
Abnormal annotation at the end of some chromosomes when using LearnModel command

#58 bio-lilin closed 3 months ago
2
Reorder genomic annotations and TSS neighborhood

#57 jmzvillarreal closed 6 months ago
2
how to choose the way of binarization, independently, concatenated or stacking?

#56 JhinAir closed 9 months ago
2
Base from OverlapEnrichment command

#55 hanrong498 closed 9 months ago
4
chromHMM input choice and annotation of external bed file

#54 cleliacort closed 11 months ago
1
Only the first 10% of the contigs outputted

#53 johannesnicolaus closed 1 year ago
2
OverlapEnrichment in LearnModel and standalone gives different results

#52 isidorabi closed 1 year ago
2
model_N.txt file clarification

#51 NMaziak closed 1 year ago
1
Error when using ConvertGeneTable function

#50 johannesnicolaus closed 8 months ago
3
ConvertGeneTable: Exception in thread "main" java.lang.IllegalArgumentException: invalid strand

#49 OscarAramburu closed 1 year ago
4
Coverage as Learnmodel input feature

#48 NickPanyushev closed 2 years ago
7
Binarized data

#47 makc-sel closed 2 years ago
2
WGBS binarization

#46 makc-sel closed 2 years ago
3
output truncates chromosomes

#45 umasstr closed 2 years ago
4
Exception in thread "main" java.lang.UnsatisfiedLinkError:

#44 El-Castor closed 2 years ago
7
Exception` in thread "main" java.util.zip.ZipException: invalid distance too far back

#43 Simple53 closed 2 years ago
4
nullpointerexception error while running CompareModels

#42 SplitInf closed 2 years ago
2
discrepancy between X_Y_overlap.png and X_Y_overlap.txt

#41 keksundso closed 2 years ago
2
Removing multi-mapping reads when using ChromHMM

#40 rauldiul closed 2 years ago
1
Compare with 2 different result

#39 dahun73 closed 3 years ago
4
Is there any suitable way to compare the states of different tissue?

#38 shangguandong1996 closed 3 years ago
1
Chromatin marks for ChIP seq data

#37 AIqbal94 closed 3 years ago
4
ChromHmm output segment file of varying segment size

#36 mujahida87 closed 3 years ago
2
ConvertGeneTable "main" java.util.NoSuchElementException

#35 yussufhajjaj closed 3 years ago
10
Credible interval of fold-enrichment (OverlapEnrichment functionality)

#34 snaketron closed 3 years ago
4
ChromHMM v1.21 errors: java.lang.OutOfMemoryError

#33 AdrijaK closed 3 years ago
2
overlap enrichment issue

#32 AicuiZhang closed 3 years ago
2
Applying segmentation analysis to ChIP-seq data from DNA binding proteins

#31 MahShaaban closed 3 years ago
4
Model fit and uncertainity of the estimates

#30 MahShaaban closed 3 years ago
4
Why is 'binarizeBed -peaks' not recommended for broad peaks?

#29 eregenyi closed 3 years ago
1
how to associate color and FoldEnrichment in OverlapEnrichment result

#28 shangguandong1996 closed 4 years ago
2
Keep reporting error when I try to run CompareModels

#27 Ruitulyu closed 4 years ago
7
error in binarizeSignal

#26 KailiBio closed 4 years ago
1
"flankwidthcontrol" in Preprocess

#25 zhangnan0107 closed 4 years ago
1
chromHMM overlap enrichments error for input string: "E"

#24 fionaandcake11 closed 4 years ago
1
ChromHMM BinarizeBam error "Permission denied"

#23 HasseB-MAN closed 4 years ago
1
Understanding of OverlapEnrichment command

#22 El-Castor closed 5 years ago
1
bam not found by BinarizeBam command

#21 El-Castor closed 5 years ago
5
NoSuchElementException in ConvertGeneTable

#20 NBKingsley closed 3 years ago
12
NullPointerException in ConvertGeneTable

#19 retropc66 closed 5 years ago
2
ChromHMM state transmissions

#18 StefanKurtenbach closed 5 years ago
1
Sliding window bins vs. separate bins

#17 snaketron closed 5 years ago
1
ChromHMM overlap enrichment

#16 josruirod closed 6 years ago
1
ChromHMM with additional genomes

#15 kernco closed 6 years ago
2
Calculation of Overlap/Neighborhood/Enrichment

#14 snaketron closed 6 years ago
1
Coordinates in CpGIsland.MSU7.bed not assigned to any state

#13 mforoozani1 closed 6 years ago
4
Push data files into git repository

#12 daissi closed 6 years ago
1
Please use release tags

#11 tillea closed 6 years ago
1