Showing : DiffHic • reset
2
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2
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1.1k
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diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
3.4 years ago nelsonmo • 0
0
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2
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1.0k
views
Can't normalize samples in diffHic
diffHic
3.4 years ago arielpaulson ▴ 20
1
vote
7
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1.9k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 30
0
votes
1
reply
1.1k
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
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1
reply
803
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 5.2 years ago by ★ 28k • written 5.3 years ago by • 0
0
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1
reply
1.3k
views
conda install of diffHic
diffHic conda
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
1
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7
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2.0k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
1
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2
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1.1k
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
0
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3
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1.3k
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 5.4 years ago by ★ 28k • written 5.4 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
5.4 years ago shopnil99 • 0
0
votes
2
replies
1.2k
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 10
0
votes
9
replies
1.8k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 10
0
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1
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1.1k
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
6.0 years ago mictadlo ▴ 10
0
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2
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888
views
Pre-processing for diffHiC
diffHiC
updated 6.2 years ago by ★ 28k • written 6.2 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 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
0
votes
3
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4.6k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 7.1 years ago by • 0 • written 9.1 years ago by • 0
2
votes
1
reply
1.4k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
0
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3
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1.5k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.2 years ago by 25k • written 7.2 years ago by • 0
0
votes
8
replies
1.9k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 20
0
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10
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2.3k
views
error running presplit_map.py
diffHic
7.2 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
7.4 years ago sergio.espeso-gil • 0
3
votes
2
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2.7k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
7.5 years ago • updated 7.4 years ago e.jacobson ▴ 10
0
votes
1
reply
838
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
0
votes
6
replies
1.5k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.7 years ago by ★ 28k • written 7.7 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 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 20
0
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1
reply
1.1k
views
diffHic count data
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
2
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7
replies
1.5k
views
diffHic: minimum counts per bin
diffhic edger
8.0 years ago andreucat91 • 0
5
votes
12
replies
3.4k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
8.0 years ago Sameet Mehta ▴ 30
1
vote
2
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1.1k
views
Removing trended biases between HiC libraries
diffhic
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 130
1
vote
3
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1.2k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 130
1
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4
replies
1.5k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 8.2 years ago by 67k • written 8.2 years ago by • 0
0
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3
replies
1.0k
views
Error in plotDI in pacakge diffHic
diffHic plotDI
8.3 years ago Andrew • 0
0
votes
1
reply
1.3k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
1
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4
replies
1.3k
views
diffHic:Fails to load bam file during preparePairs
diffhic
8.3 years ago manjulathimma • 0
0
votes
2
replies
1.1k
views
generate ContactMatrix from InteractionSet object
diffhic
8.3 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 8.3 years ago by • 0 • written 8.3 years ago by • 0
1
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5
replies
1.6k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
8.4 years ago Vivek.b ▴ 100
0
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3
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1.3k
views
diffHic: alternative input?
diffhic
8.4 years ago chiara.a.nicoletti • 0
0
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1
reply
1.2k
views
diffHic preparePairs function
diffHic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
0
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1
reply
1.0k
views
diffHiC: Error when call preparePairs
diffhic
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
0
votes
1
reply
1.0k
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
0
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1
reply
906
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 20
1
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3
replies
1.2k
views
diffHiC preparePairs error
diffhic preparepairs
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 20
0
votes
1
reply
1.1k
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
1
vote
1
reply
1.7k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 130
1
vote
5
replies
1.9k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.9 years ago by ★ 28k • written 8.9 years ago by • 0
0
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1
reply
1.2k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 9.1 years ago by ★ 28k • written 9.1 years ago by • 0
0
votes
1
reply
1.2k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 9.1 years ago by ★ 28k • written 9.1 years ago by • 0
1
vote
3
replies
1.4k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
9.1 years ago roladali ▴ 20
0
votes
6
replies
1.9k
views
diffHic preparepairs issue
diffhic
9.2 years ago fine418 • 0
50 results • Page 1 of 1
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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