Showing : diffHic • reset
2
votes
2
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460
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
18 months ago nelsonmo • 0
0
votes
2
replies
479
views
Can't normalize samples in diffHic
diffHic
19 months ago • updated 18 months ago arielpaulson ▴ 20
1
vote
7
replies
957
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ▴ 30
0
votes
1
reply
422
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 2.8 years ago by ★ 28k • written 2.8 years ago by • 0
0
votes
1
reply
354
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 3.4 years ago by ★ 28k • written 3.4 years ago by • 0
0
votes
1
reply
601
views
conda install of diffHic
diffHic conda
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
1
vote
7
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954
views
Error while running normOffsets in diffhic
diffhic csaw
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
1
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2
replies
548
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
0
votes
3
replies
610
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 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
2
votes
3
replies
642
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
3.6 years ago shopnil99 • 0
0
votes
2
replies
527
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 10
0
votes
9
replies
777
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
0
votes
1
reply
519
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
4.2 years ago • updated 4.1 years ago mictadlo ▴ 10
0
votes
2
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459
views
Pre-processing for diffHiC
diffHiC
updated 4.3 years ago by ★ 28k • written 4.3 years ago by 62k
1
vote
1
reply
805
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
0
votes
3
replies
3.7k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 5.2 years ago by • 0 • written 7.3 years ago by • 0
2
votes
1
reply
708
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
0
votes
3
replies
873
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
0
votes
8
replies
945
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
0
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10
replies
1.3k
views
error running presplit_map.py
diffHic
5.3 years ago Eichan • 0
2
votes
2
replies
997
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
5.5 years ago sergio.espeso-gil • 0
2
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2
replies
1.8k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
5.6 years ago • updated 5.5 years ago e.jacobson • 0
0
votes
1
reply
524
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
0
votes
6
replies
918
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 20
2
votes
1
reply
928
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 20
0
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1
reply
729
views
diffHic count data
diffhic
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 10
2
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7
replies
869
views
diffHic: minimum counts per bin
diffhic edger
6.1 years ago andreucat91 • 0
5
votes
12
replies
2.0k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
6.2 years ago • updated 6.1 years ago Sameet Mehta ▴ 30
1
vote
2
replies
695
views
Removing trended biases between HiC libraries
diffhic
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 120
1
vote
3
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801
views
Interpreting strand orientation plots in diffHic
diffhic
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 120
1
vote
4
replies
1.0k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 6.3 years ago by 62k • written 6.3 years ago by • 0
0
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3
replies
688
views
Error in plotDI in pacakge diffHic
diffHic plotDI
6.4 years ago Andrew • 0
0
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1
reply
791
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
1
vote
4
replies
811
views
diffHic:Fails to load bam file during preparePairs
diffhic
6.4 years ago manjulathimma • 0
0
votes
2
replies
698
views
generate ContactMatrix from InteractionSet object
diffhic
6.4 years ago kamal.fartiyal84 ▴ 10
1
vote
3
replies
995
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 6.5 years ago by • 0 • written 6.5 years ago by • 0
1
vote
5
replies
960
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
6.5 years ago Vivek.b ▴ 100
0
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3
replies
859
views
diffHic: alternative input?
diffhic
6.5 years ago chiara.a.nicoletti • 0
0
votes
1
reply
730
views
diffHic preparePairs function
diffHic
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
0
votes
1
reply
650
views
diffHiC: Error when call preparePairs
diffhic
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
0
votes
1
reply
643
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
0
votes
1
reply
577
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 20
1
vote
3
replies
756
views
diffHiC preparePairs error
diffhic preparepairs
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 20
0
votes
1
reply
689
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
1
vote
1
reply
1.2k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 120
0
votes
5
replies
1.2k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 7.0 years ago by ★ 28k • written 7.0 years ago by • 0
0
votes
1
reply
878
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
0
votes
1
reply
754
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
1
vote
3
replies
958
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
7.2 years ago roladali ▴ 20
0
votes
6
replies
1.2k
views
diffHic preparepairs issue
diffhic
7.4 years ago fine418 • 0
50 results • Page 1 of 1
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Answer: struggling to create a heatmap by ATpoint ★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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