Showing : diffHic • reset
2
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2
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1.3k
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diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
4.1 years ago nelsonmo • 0
0
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2
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1.2k
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Can't normalize samples in diffHic
diffHic
4.1 years ago arielpaulson ▴ 20
1
vote
7
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2.2k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 5.0 years ago by ★ 29k • written 5.0 years ago by ▴ 30
0
votes
1
reply
1.2k
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How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 5.3 years ago by ★ 29k • written 5.4 years ago by • 0
0
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1
reply
972
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 5.9 years ago by ★ 29k • written 5.9 years ago by • 0
0
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1
reply
1.5k
views
conda install of diffHic
diffHic conda
updated 6.0 years ago by ★ 29k • written 6.1 years ago by • 0
1
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7
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2.4k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 6.1 years ago by ★ 29k • written 6.1 years ago by • 0
1
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2
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1.3k
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 6.1 years ago by ★ 29k • written 6.1 years ago by • 0
0
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3
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1.6k
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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 6.1 years ago by ★ 29k • written 6.1 years ago by • 0
2
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3
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1.4k
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diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
6.1 years ago shopnil99 • 0
0
votes
2
replies
1.4k
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 6.4 years ago by ★ 29k • written 6.4 years ago by ▴ 10
0
votes
9
replies
2.2k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 10
0
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1
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1.2k
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Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
6.7 years ago mictadlo ▴ 10
0
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2
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1.0k
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Pre-processing for diffHiC
diffHiC
updated 6.9 years ago by ★ 29k • written 6.9 years ago by 68k
1
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1
reply
2.0k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
0
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3
replies
5.0k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 7.8 years ago by • 0 • written 9.8 years ago by • 0
2
votes
1
reply
1.6k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 20
0
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3
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1.7k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 7.9 years ago by 25k • written 7.9 years ago by • 0
0
votes
8
replies
2.2k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 20
0
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10
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2.7k
views
error running presplit_map.py
diffHic
7.9 years ago Eichan • 0
2
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2
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1.8k
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Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
8.1 years ago sergio.espeso-gil • 0
3
votes
2
replies
3.1k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
8.2 years ago • updated 8.1 years ago e.jacobson ▴ 10
0
votes
1
reply
973
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
0
votes
6
replies
1.7k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 20
2
votes
1
reply
1.6k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 20
0
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1
reply
1.2k
views
diffHic count data
diffhic
updated 8.6 years ago by ★ 29k • written 8.6 years ago by ▴ 10
2
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7
replies
1.7k
views
diffHic: minimum counts per bin
diffhic edger
8.7 years ago andreucat91 • 0
5
votes
12
replies
3.9k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
8.7 years ago Sameet Mehta ▴ 30
1
vote
2
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1.2k
views
Removing trended biases between HiC libraries
diffhic
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 130
1
vote
3
replies
1.4k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 130
1
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4
replies
1.6k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
0
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3
replies
1.1k
views
Error in plotDI in pacakge diffHic
diffHic plotDI
9.0 years ago Andrew • 0
0
votes
1
reply
1.4k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 9.0 years ago by ★ 29k • written 9.0 years ago by • 0
1
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4
replies
1.4k
views
diffHic:Fails to load bam file during preparePairs
diffhic
9.0 years ago manjulathimma • 0
0
votes
2
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1.3k
views
generate ContactMatrix from InteractionSet object
diffhic
9.0 years ago kamal.fartiyal84 ▴ 10
1
vote
3
replies
1.9k
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 9.0 years ago by • 0 • written 9.0 years ago by • 0
1
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5
replies
1.8k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
9.1 years ago Vivek.b ▴ 100
0
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3
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1.5k
views
diffHic: alternative input?
diffhic
9.1 years ago chiara.a.nicoletti • 0
0
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1
reply
1.3k
views
diffHic preparePairs function
diffHic
updated 9.1 years ago by ★ 29k • written 9.1 years ago by • 0
0
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1
reply
1.1k
views
diffHiC: Error when call preparePairs
diffhic
updated 9.2 years ago by ★ 29k • written 9.2 years ago by • 0
0
votes
1
reply
1.1k
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 9.2 years ago by ★ 29k • written 9.2 years ago by • 0
0
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1
reply
1.0k
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 9.2 years ago by ★ 29k • written 9.2 years ago by ▴ 20
1
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3
replies
1.4k
views
diffHiC preparePairs error
diffhic preparepairs
updated 9.3 years ago by ★ 29k • written 9.3 years ago by ▴ 20
0
votes
1
reply
1.2k
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
1
vote
1
reply
1.9k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 9.3 years ago by ★ 29k • written 9.3 years ago by ▴ 130
1
vote
5
replies
2.2k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 9.6 years ago by ★ 29k • written 9.6 years ago by • 0
0
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1
reply
1.3k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
0
votes
1
reply
1.3k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 9.8 years ago by ★ 29k • written 9.8 years ago by • 0
1
vote
3
replies
1.5k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
9.8 years ago roladali ▴ 20
0
votes
6
replies
2.1k
views
diffHic preparepairs issue
diffhic
9.9 years ago fine418 • 0
55 results • Page 1 of 2
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Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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