Showing : diffHic • reset
5
votes
12
replies
2.9k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
7.4 years ago Sameet Mehta ▴ 30
4
votes
20
replies
2.4k
views
scaling loess curves
HiTC gothic diffhic HiC
8.6 years ago Bogdan ▴ 670
3
votes
2
replies
2.3k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
6.8 years ago e.jacobson ▴ 10
2
votes
4
replies
1.7k
views
diffHic-package_PreparePairs-function-error:"missing chromosomes in cut site list"
diffHic PreparePairs Hi-c cutGenome
8.9 years ago • updated 8.8 years ago rulicosentino • 0
2
votes
1
reply
1.2k
views
diffHiC with no biological replicates?
diffhic estimate dispersion value glm no replicates deseq
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
6.7 years ago sergio.espeso-gil • 0
2
votes
1
reply
1.2k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 20
2
votes
1
reply
1.2k
views
How to read in bam file that is output from presplit_map.py using the GenomicAlignment package
diffhic
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 30
2
votes
3
replies
999
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
4.8 years ago shopnil99 • 0
2
votes
7
replies
1.2k
views
diffHic: minimum counts per bin
diffhic edger
7.4 years ago andreucat91 • 0
2
votes
2
replies
842
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
2.8 years ago nelsonmo • 0
1
vote
3
replies
1.0k
views
diffHiC preparePairs error
diffhic preparepairs
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
1
vote
5
replies
1.7k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
1
vote
3
replies
1.2k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
8.4 years ago roladali ▴ 20
1
vote
4
replies
1.3k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 7.5 years ago by 65k • written 7.5 years ago by • 0
1
vote
7
replies
1.6k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 30
1
vote
3
replies
1.1k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 120
1
vote
2
replies
863
views
rotPlaid error "Error in if (x.min >= x.max) { : missing value where TRUE/FALSE needed"
diffhic rotPlaid
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
7
replies
1.6k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
1
vote
2
replies
922
views
Removing trended biases between HiC libraries
diffhic
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 120
1
vote
5
replies
1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
7.7 years ago Vivek.b ▴ 100
1
vote
3
replies
1.4k
views
diffHic: How to remove extra chromosomes like chrUn_gl00* from pairParam object
diffHic
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
1
vote
4
replies
1.1k
views
diffHic:Fails to load bam file during preparePairs
diffhic
7.7 years ago • updated 7.6 years ago manjulathimma • 0
1
vote
1
reply
1.5k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 120
1
vote
1
reply
1.3k
views
extract HiC contacts for a given BEDPE set of coordinates
hic diffhic chromatin bedpe
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
0
votes
2
replies
890
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
0
votes
3
replies
1.0k
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 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
0
votes
1
reply
1.1k
views
conda install of diffHic
diffHic conda
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
votes
1
reply
635
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
0
votes
1
reply
823
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
0
votes
2
replies
788
views
Can't normalize samples in diffHic
diffHic
2.8 years ago arielpaulson ▴ 20
0
votes
1
reply
1.1k
views
DiffHic-package. Identify the name of bins with over or underrepresentation of reads mapped -marginCounts- . Extracting data from DIList objects
MarginCounts squareCounts DIList DiffHic
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
votes
2
replies
1.5k
views
diffHiC read loss when loading BAM to HDF
diffhic
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
votes
6
replies
1.7k
views
diffHic preparepairs issue
diffhic
8.6 years ago fine418 • 0
0
votes
3
replies
4.2k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 6.4 years ago by • 0 • written 8.5 years ago by • 0
0
votes
1
reply
998
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
0
votes
1
reply
1.0k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
0
votes
1
reply
910
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
772
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
0
votes
1
reply
865
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
1
reply
871
views
diffHiC: Error when call preparePairs
diffhic
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
1
reply
1.0k
views
diffHic preparePairs function
diffHic
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
3
replies
1.1k
views
diffHic: alternative input?
diffhic
7.8 years ago • updated 7.7 years ago chiara.a.nicoletti • 0
0
votes
2
replies
980
views
generate ContactMatrix from InteractionSet object
diffhic
7.6 years ago kamal.fartiyal84 ▴ 10
0
votes
3
replies
891
views
Error in plotDI in pacakge diffHic
diffHic plotDI
7.6 years ago Andrew • 0
0
votes
1
reply
1.1k
views
How to run plotPlaid in diffHic Package using output from hic Pro
plotPlaid diffHic
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
0
votes
1
reply
969
views
diffHic count data
diffhic
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 10
0
votes
6
replies
1.3k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 20
0
votes
1
reply
703
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
0
votes
10
replies
1.9k
views
error running presplit_map.py
diffHic
6.5 years ago Eichan • 0
50 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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