Showing : diffHiC • reset
2
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diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
3.3 years ago nelsonmo • 0
0
votes
2
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976
views
Can't normalize samples in diffHic
diffHic
3.3 years ago arielpaulson ▴ 20
1
vote
7
replies
1.8k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 30
0
votes
1
reply
1.0k
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.5 years ago by ★ 28k • written 4.6 years ago by • 0
0
votes
1
reply
779
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
0
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1
reply
1.3k
views
conda install of diffHic
diffHic conda
updated 5.2 years ago by ★ 28k • written 5.3 years ago by • 0
1
vote
7
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2.0k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
1
vote
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 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
0
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3
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1.3k
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diffHic presplit_map.py --sig option for HiC libraries prepared with restriction enzyme cocktail from Arima genomics
diffhic Arima Genomics presplit_map.py
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
2
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3
replies
1.2k
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
5.3 years ago shopnil99 • 0
0
votes
2
replies
1.1k
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.6 years ago by ★ 28k • written 5.6 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 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 10
0
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1
reply
1.1k
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
5.9 years ago mictadlo ▴ 10
0
votes
2
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872
views
Pre-processing for diffHiC
diffHiC
updated 6.1 years ago by ★ 28k • written 6.1 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 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
0
votes
3
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4.5k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 7.0 years ago by • 0 • written 9.0 years ago by • 0
2
votes
1
reply
1.4k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 20
0
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3
replies
1.5k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.1 years ago by 25k • written 7.1 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 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
0
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10
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2.2k
views
error running presplit_map.py
diffHic
7.1 years ago Eichan • 0
2
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2
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1.6k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
7.3 years ago sergio.espeso-gil • 0
3
votes
2
replies
2.6k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
7.4 years ago • updated 7.3 years ago e.jacobson ▴ 10
0
votes
1
reply
819
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
0
votes
6
replies
1.5k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.6 years ago by ★ 28k • written 7.6 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 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 20
0
votes
1
reply
1.1k
views
diffHic count data
diffhic
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 10
2
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7
replies
1.4k
views
diffHic: minimum counts per bin
diffhic edger
7.9 years ago andreucat91 • 0
5
votes
12
replies
3.3k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
7.9 years ago Sameet Mehta ▴ 30
1
vote
2
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1.1k
views
Removing trended biases between HiC libraries
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 130
1
vote
3
replies
1.2k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 130
1
vote
4
replies
1.5k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 8.1 years ago by 67k • written 8.1 years ago by • 0
0
votes
3
replies
1.0k
views
Error in plotDI in pacakge diffHic
diffHic plotDI
8.2 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 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
1
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4
replies
1.2k
views
diffHic:Fails to load bam file during preparePairs
diffhic
8.2 years ago manjulathimma • 0
0
votes
2
replies
1.1k
views
generate ContactMatrix from InteractionSet object
diffhic
8.2 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 8.2 years ago by • 0 • written 8.2 years ago by • 0
1
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5
replies
1.5k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
8.3 years ago Vivek.b ▴ 100
0
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3
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1.3k
views
diffHic: alternative input?
diffhic
8.3 years ago chiara.a.nicoletti • 0
0
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1
reply
1.2k
views
diffHic preparePairs function
diffHic
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
0
votes
1
reply
994
views
diffHiC: Error when call preparePairs
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
0
votes
1
reply
1.0k
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
0
votes
1
reply
890
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 20
1
vote
3
replies
1.2k
views
diffHiC preparePairs error
diffhic preparepairs
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 20
0
votes
1
reply
1.0k
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
1
vote
1
reply
1.7k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 130
1
vote
5
replies
1.9k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
0
votes
1
reply
1.2k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 9.0 years ago by ★ 28k • written 9.0 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 9.0 years ago by ★ 28k • written 9.0 years ago by • 0
1
vote
3
replies
1.3k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
9.0 years ago roladali ▴ 20
0
votes
6
replies
1.8k
views
diffHic preparepairs issue
diffhic
9.1 years ago fine418 • 0
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Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Comment: makeContrastsDream for Interaction by abadgerw • 0
@gabrielhoffman any insight?
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by Michael Love 42k
That is the rows that did converge.
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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