Showing : diffHiC • reset
5
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12
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3.0k
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How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
7.4 years ago Sameet Mehta ▴ 30
4
votes
20
replies
2.5k
views
scaling loess curves
HiTC gothic diffhic HiC
8.7 years ago Bogdan ▴ 670
3
votes
2
replies
2.4k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
6.9 years ago • updated 6.8 years ago e.jacobson ▴ 10
2
votes
4
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1.8k
views
diffHic-package_PreparePairs-function-error:"missing chromosomes in cut site list"
diffHic PreparePairs Hi-c cutGenome
8.9 years ago rulicosentino • 0
2
votes
1
reply
1.2k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
6.8 years ago sergio.espeso-gil • 0
2
votes
1
reply
1.2k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 20
2
votes
1
reply
1.2k
views
How to read in bam file that is output from presplit_map.py using the GenomicAlignment package
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 30
2
votes
3
replies
1.0k
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
4.8 years ago shopnil99 • 0
2
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7
replies
1.2k
views
diffHic: minimum counts per bin
diffhic edger
7.4 years ago andreucat91 • 0
2
votes
2
replies
858
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
2.8 years ago nelsonmo • 0
1
vote
3
replies
1.0k
views
diffHiC preparePairs error
diffhic preparepairs
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
1
vote
5
replies
1.7k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
1
vote
3
replies
1.2k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
8.5 years ago roladali ▴ 20
1
vote
4
replies
1.3k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 7.6 years ago by 65k • written 7.6 years ago by • 0
1
vote
7
replies
1.6k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 30
1
vote
3
replies
1.1k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 120
1
vote
2
replies
875
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
2
replies
931
views
Removing trended biases between HiC libraries
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 120
1
vote
5
replies
1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
7.8 years ago Vivek.b ▴ 100
1
vote
3
replies
1.4k
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
1
vote
4
replies
1.1k
views
diffHic:Fails to load bam file during preparePairs
diffhic
7.7 years ago • updated 7.6 years ago manjulathimma • 0
1
vote
1
reply
1.5k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 120
1
vote
1
reply
1.4k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
0
votes
2
replies
905
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
0
votes
3
replies
1.0k
views
diffHic presplit_map.py --sig option for HiC libraries prepared with restriction enzyme cocktail from Arima genomics
diffhic Arima Genomics presplit_map.py
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
0
votes
1
reply
1.1k
views
conda install of diffHic
diffHic conda
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
votes
1
reply
647
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
0
votes
1
reply
840
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
0
votes
2
replies
799
views
Can't normalize samples in diffHic
diffHic
2.8 years ago arielpaulson ▴ 20
0
votes
1
reply
1.1k
views
DiffHic-package. Identify the name of bins with over or underrepresentation of reads mapped -marginCounts- . Extracting data from DIList objects
MarginCounts squareCounts DIList DiffHic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
0
votes
2
replies
1.5k
views
diffHiC read loss when loading BAM to HDF
diffhic
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
votes
6
replies
1.7k
views
diffHic preparepairs issue
diffhic
8.6 years ago fine418 • 0
0
votes
3
replies
4.3k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 6.5 years ago by • 0 • written 8.5 years ago by • 0
0
votes
1
reply
1.0k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
0
votes
1
reply
1.1k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
0
votes
1
reply
919
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
0
votes
1
reply
779
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
0
votes
1
reply
872
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
879
views
diffHiC: Error when call preparePairs
diffhic
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
1
reply
1.0k
views
diffHic preparePairs function
diffHic
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
3
replies
1.2k
views
diffHic: alternative input?
diffhic
7.8 years ago chiara.a.nicoletti • 0
0
votes
2
replies
991
views
generate ContactMatrix from InteractionSet object
diffhic
7.7 years ago kamal.fartiyal84 ▴ 10
0
votes
3
replies
899
views
Error in plotDI in pacakge diffHic
diffHic plotDI
7.6 years ago Andrew • 0
0
votes
1
reply
1.1k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
0
votes
1
reply
980
views
diffHic count data
diffhic
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 10
0
votes
6
replies
1.3k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 20
0
votes
1
reply
709
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
0
votes
10
replies
1.9k
views
error running presplit_map.py
diffHic
6.6 years ago • updated 6.5 years ago Eichan • 0
50 results • Page 1 of 1
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Replies
Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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