Showing : DiffHic • reset
2
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2
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1.0k
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diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
3.2 years ago nelsonmo • 0
0
votes
2
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952
views
Can't normalize samples in diffHic
diffHic
3.2 years ago arielpaulson ▴ 20
1
vote
7
replies
1.8k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 30
0
votes
1
reply
995
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
0
votes
1
reply
751
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
0
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1
reply
1.3k
views
conda install of diffHic
diffHic conda
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
1
vote
7
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1.9k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
1
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2
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1.0k
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
0
votes
3
replies
1.2k
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 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
2
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3
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1.2k
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
5.2 years ago shopnil99 • 0
0
votes
2
replies
1.1k
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 10
0
votes
9
replies
1.7k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 10
0
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1
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1.0k
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
5.8 years ago mictadlo ▴ 10
0
votes
2
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841
views
Pre-processing for diffHiC
diffHiC
updated 5.9 years ago by ★ 28k • written 5.9 years ago by 67k
1
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1
reply
1.6k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
0
votes
3
replies
4.5k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 6.9 years ago by • 0 • written 8.9 years ago by • 0
2
votes
1
reply
1.4k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 6.9 years ago by ★ 28k • written 6.9 years ago by ▴ 20
0
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3
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1.4k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 6.9 years ago by 25k • written 6.9 years ago by • 0
0
votes
8
replies
1.8k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 20
0
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10
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2.2k
views
error running presplit_map.py
diffHic
7.0 years ago Eichan • 0
2
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2
replies
1.6k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
7.2 years ago sergio.espeso-gil • 0
3
votes
2
replies
2.5k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
7.3 years ago • updated 7.2 years ago e.jacobson ▴ 10
0
votes
1
reply
798
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
0
votes
6
replies
1.5k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
2
votes
1
reply
1.4k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
0
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1
reply
1.1k
views
diffHic count data
diffhic
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 10
2
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7
replies
1.4k
views
diffHic: minimum counts per bin
diffhic edger
7.8 years ago andreucat91 • 0
5
votes
12
replies
3.2k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
7.8 years ago Sameet Mehta ▴ 30
1
vote
2
replies
1.0k
views
Removing trended biases between HiC libraries
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 130
1
vote
3
replies
1.2k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 130
1
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4
replies
1.4k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 8.0 years ago by 67k • written 8.0 years ago by • 0
0
votes
3
replies
986
views
Error in plotDI in pacakge diffHic
diffHic plotDI
8.0 years ago Andrew • 0
0
votes
1
reply
1.2k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
1
vote
4
replies
1.2k
views
diffHic:Fails to load bam file during preparePairs
diffhic
8.1 years ago • updated 8.0 years ago manjulathimma • 0
0
votes
2
replies
1.1k
views
generate ContactMatrix from InteractionSet object
diffhic
8.1 years ago kamal.fartiyal84 ▴ 10
1
vote
3
replies
1.6k
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 8.1 years ago by • 0 • written 8.1 years ago by • 0
1
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5
replies
1.5k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
8.2 years ago Vivek.b ▴ 100
0
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3
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1.2k
views
diffHic: alternative input?
diffhic
8.2 years ago chiara.a.nicoletti • 0
0
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1
reply
1.1k
views
diffHic preparePairs function
diffHic
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
0
votes
1
reply
974
views
diffHiC: Error when call preparePairs
diffhic
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
0
votes
1
reply
973
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
0
votes
1
reply
873
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 20
1
vote
3
replies
1.2k
views
diffHiC preparePairs error
diffhic preparepairs
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 20
0
votes
1
reply
1.0k
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
1
vote
1
reply
1.6k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 130
1
vote
5
replies
1.9k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
0
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1
reply
1.1k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
0
votes
1
reply
1.1k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 8.9 years ago by ★ 28k • written 8.9 years ago by • 0
1
vote
3
replies
1.3k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
8.9 years ago roladali ▴ 20
0
votes
6
replies
1.8k
views
diffHic preparepairs issue
diffhic
9.0 years ago fine418 • 0
50 results • Page 1 of 1
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Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Hi Maria, so what is the code you are using? By the 3rd way to conduct the analysis do you mean looking at the interaction model from part …
Comment: miRTarRnaseq library by María Calvo • 0
Hello, in line with the previous questions, when the miRNA-mRNA interaction analysis is performed (3 rd way to conduct the analysis), I obt…
Answer: heatmap with batch effect by James W. MacDonald 67k
You have only one condition in the second batch, so it's not possible to remove the batch effect. You can probably adjust for it somewhat, …
Answer: how do I convert an Ilumn IDREF to a CPG loci by James W. MacDonald 67k
``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame with 865859 rows and 3 columns ch…
Answer: Which input data is acceptable for MAST? by Andrew_McDavid ▴ 270
Not too familiar with SCT v2. If it also has a point-mass at zero and the non-zero component is roughly-symmetric, then it might work ok w…
Votes
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Comment: Convert HGVS Representation back to Reference Genome Coordinates
Answer: How to control batch effect if Group and batch are same?
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