Showing : diffHic • reset
2
votes
2
replies
864
views
diffHic's totalCounts fails with multiple files, but rest of test code works
diffHic
2.8 years ago nelsonmo • 0
0
votes
2
replies
804
views
Can't normalize samples in diffHic
diffHic
2.9 years ago • updated 2.8 years ago arielpaulson ▴ 20
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
0
votes
1
reply
847
views
How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.1 years ago by ★ 28k • written 4.1 years ago by • 0
0
votes
1
reply
656
views
diffHiC error in mergePairs.
diffHiC rdhf5
updated 4.6 years ago by ★ 28k • written 4.7 years ago by • 0
0
votes
1
reply
1.1k
views
conda install of diffHic
diffHic conda
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
7
replies
1.7k
views
Error while running normOffsets in diffhic
diffhic csaw
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
2
replies
883
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
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
2
votes
3
replies
1.0k
views
diffHic presplit_map.py pysam.SamtoolsError
diffHic pysam.SamtoolsError pysam.sort
4.8 years ago shopnil99 • 0
0
votes
2
replies
912
views
diffHic ICE normalization PCA with NAs
diffHic normalization pca NAs HI-C
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
0
votes
9
replies
1.5k
views
from denove contig assembly to chromosome bins
diffhic gothic hicup hic-c hic
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 10
0
votes
1
reply
914
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic diffhic gothic hicup hic-c
5.5 years ago • updated 5.4 years ago mictadlo ▴ 10
0
votes
2
replies
734
views
Pre-processing for diffHiC
diffHiC
updated 5.6 years ago by ★ 28k • written 5.6 years ago by 65k
1
vote
1
reply
1.4k
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
3
replies
4.3k
views
Error while processing BAM file with Picard FixMateInformation
diffHic diffhic
updated 6.5 years ago by • 0 • written 8.5 years ago by • 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
0
votes
3
replies
1.3k
views
csaw intallation issue: cannot find "lib" in Rhtslib installation
diffhic csaw Rhtslib
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
0
votes
8
replies
1.6k
views
How to get specific fragment/read interactions from HiC (diffHiC) data?
diffhic hic
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
0
votes
10
replies
1.9k
views
error running presplit_map.py
diffHic
6.6 years ago Eichan • 0
2
votes
2
replies
1.4k
views
Extracting non-interacting hic reads to create a sam/bam file
diffhic hicpro hic
6.8 years ago sergio.espeso-gil • 0
3
votes
2
replies
2.4k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup hi-c diffhic homer
6.9 years ago • updated 6.8 years ago e.jacobson ▴ 10
0
votes
1
reply
715
views
How to do normalization between different enzyme libraries and test the difference by diffHic.
diffhic
updated 7.0 years ago by ★ 28k • written 7.0 years ago by • 0
0
votes
6
replies
1.3k
views
min enrichment in peak calling with diffHiC?
diffhic peak
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
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
0
votes
1
reply
984
views
diffHic count data
diffhic
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 10
2
votes
7
replies
1.3k
views
diffHic: minimum counts per bin
diffhic edger
7.4 years ago andreucat91 • 0
5
votes
12
replies
3.0k
views
How to use diffHiC with existing contact matrices?
diffHiC HiCPro diffhic
7.4 years ago Sameet Mehta ▴ 30
1
vote
2
replies
937
views
Removing trended biases between HiC libraries
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 120
1
vote
3
replies
1.1k
views
Interpreting strand orientation plots in diffHic
diffhic
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 120
1
vote
4
replies
1.3k
views
Problem in finding NB dispersion for my HiC datasets
diffhic
updated 7.6 years ago by 65k • written 7.6 years ago by • 0
0
votes
3
replies
904
views
Error in plotDI in pacakge diffHic
diffHic plotDI
7.7 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 7.7 years ago by ★ 28k • 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 manjulathimma • 0
0
votes
2
replies
996
views
generate ContactMatrix from InteractionSet object
diffhic
7.7 years ago kamal.fartiyal84 ▴ 10
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
5
replies
1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
7.8 years ago Vivek.b ▴ 100
0
votes
3
replies
1.2k
views
diffHic: alternative input?
diffhic
7.8 years ago chiara.a.nicoletti • 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
1
reply
886
views
diffHiC: Error when call preparePairs
diffhic
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
877
views
diffHiC statistical test to check differences between conditions
diffHiC statistical test
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
0
votes
1
reply
784
views
diffHiC-analyzing HiC experiments prepared with different enzymes
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 20
1
vote
3
replies
1.0k
views
diffHiC preparePairs error
diffhic preparepairs
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 20
0
votes
1
reply
925
views
diffHic - incorporating NB-loess, CNV, and ICE offset into DGEList object
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
1
vote
1
reply
1.5k
views
Loading a precomputed interaction matrix into diffHiC
diffhic
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 120
1
vote
5
replies
1.7k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
0
votes
1
reply
1.1k
views
DiffHic package - heatmap generation from normalized data
diffhic
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
0
votes
1
reply
1.0k
views
diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
diffhic GRanges
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
1
vote
3
replies
1.2k
views
saving raw interaction matrices using diffHic
diffhic interaction matrix
8.5 years ago roladali ▴ 20
0
votes
6
replies
1.7k
views
diffHic preparepairs issue
diffhic
8.6 years ago fine418 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Locations • All
India, 31 minutes ago
Singapore, 37 minutes ago
Ireland, 1 hour ago
Hong Kong, 1 hour ago
Israel, 1 hour ago
Traffic: 299 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6