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questions
1
vote
2
replies
676
views
Transcript feature coverage with coverage of each feature shown like e.g. UTR's CDS, exons etc
rseqc
updated 3 months ago by
Huiyang
▴ 190 • written 14 months ago by
Saad Khan
▴ 440
0
votes
0
replies
227
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
5 months ago by
Saad Khan
▴ 440
5
votes
3
replies
2.3k
views
How to visualize the co-occupancy of one set of genomic data with another.
TFBS
methylation
co-occupancy
Histone
updated 2.2 years ago by
Ram
44k • written 9.6 years ago by
Saad Khan
▴ 440
0
votes
0
replies
984
views
Is it possible to introduce mutations (SNV/Indels) in precomputed lastz alignments
FastaAlternateReferenceMaker
lastz
pairwise_align
4.7 years ago by
Saad Khan
▴ 440
0
votes
2
replies
1.3k
views
Merging variant calls of whole exome and RNA-seq
GATK
RNA-seq
variants
indels
SNVs
updated 5.2 years ago by
Omics data mining
▴ 260 • written 5.2 years ago by
Saad Khan
▴ 440
1
vote
4
replies
1.6k
views
Negative dataset selection
machine-learning
sequence classification
RNA
DNA
5.3 years ago by
Saad Khan
▴ 440
0
votes
1
reply
3.6k
views
How to do gene enrichment analysis using only GO-slim terma
GO-slim
gene enrichment
updated 5.5 years ago by
EpiExplorer
▴ 90 • written 7.6 years ago by
Saad Khan
▴ 440
0
votes
1
reply
1.3k
views
Which tool to use to get all citations of a pmid paper?
entrez eutils
efetch
updated 5.6 years ago by
h.mon
35k • written 5.6 years ago by
Saad Khan
▴ 440
0
votes
0
replies
1.1k
views
Tool for generating Physicochemical properties from sequence of RNA/DNA
mRNA
DNA
Sequence
physicochemical properties
6.1 years ago by
Saad Khan
▴ 440
0
votes
3
replies
1.7k
views
Most genes with entrez id in KEGG database don't have a pathway assigned. Is there a tool already available that uses textmining to assign pathway to…
kegg
reactome
keggrest
6.2 years ago by
Saad Khan
▴ 440
0
votes
6
replies
4.3k
views
Where all can I find Histone Modification data for certain Human and Mouse cells
histone-modification
Human
Mouse
updated 3.1 years ago by
Ram
44k • written 9.6 years ago by
Saad Khan
▴ 440
1
vote
13
replies
2.9k
views
Normalization scheme to use for upstream sequences read count in (Chip-seq histones)
normalization
RPKM
histones
updated 22 months ago by
Ram
44k • written 8.4 years ago by
Saad Khan
▴ 440
0
votes
2
replies
1.4k
views
Protein protein interaction conservation scores
PPI
conservation
scores
7.2 years ago by
Saad Khan
▴ 440
0
votes
1
reply
1.5k
views
Cancer data for histone Chip-seq in human and mouse
cancer
chip-seq
histone
GEO
SRA
updated 7.2 years ago by
Ben
▴ 60 • written 7.2 years ago by
Saad Khan
▴ 440
2
votes
4
replies
2.4k
views
Clustering using codon usage similarity
codon usage
clustering
updated 7.5 years ago by
Biostar
20 • written 7.6 years ago by
Saad Khan
▴ 440
0
votes
0
replies
1.7k
views
What does mm10-minimal mean in encode files
metadata
encode
mm10-minimal
7.5 years ago by
Saad Khan
▴ 440
0
votes
0
replies
1.3k
views
Segment genes into functional subsets
gene ontology
functions
subsets
7.8 years ago by
Saad Khan
▴ 440
1
vote
0
replies
1.7k
views
Top 20% expressed orthologus genes in two species
RNA-seq
RPKM
FPKM
updated 7.8 years ago by
Biostar
20 • written 7.9 years ago by
Saad Khan
▴ 440
1
vote
0
replies
1.6k
views
Comparing features of high expression genes vs low expression genes in two species
rpkm
gene expression
RNA-Seq
7.9 years ago by
Saad Khan
▴ 440
1
vote
4
replies
2.8k
views
NIH roadmap epigenomics data Bam files
NIH
roadmap-epigenomics
updated 8.0 years ago by
Denise CS
★ 5.2k • written 8.0 years ago by
Saad Khan
▴ 440
1
vote
0
replies
1.7k
views
Statistically robust approach of assigning presence or absence of Histone peaks
Histone
Peaks
cross-species
orthologus regions
8.2 years ago by
Saad Khan
▴ 440
0
votes
2
replies
1.9k
views
What are some of the state of the art approaches for prediction of origins of replication in vertebrates
Machine learning
ORiC
origin of replication
updated 8.2 years ago by
matted
7.8k • written 8.2 years ago by
Saad Khan
▴ 440
0
votes
6
replies
2.7k
views
chain files for mouse mm9 to ensembl version 75
bed
liftover
ucsc
chain-files
ensembl
updated 22 months ago by
Ram
44k • written 8.3 years ago by
Saad Khan
▴ 440
0
votes
4
replies
3.6k
views
liftover chain files for mouse mm9 to ensembl version 75
lift-over
chain-file
mm9
ensembl
updated 22 months ago by
Ram
44k • written 8.3 years ago by
Saad Khan
▴ 440
5
votes
5
replies
3.3k
views
Where are the actual transcription factor binding sites located in the CHIP-seq peaks
CHIP-seq-peaks
MACS
peak-calls
TFBS
updated 21 months ago by
Ram
44k • written 8.6 years ago by
Saad Khan
▴ 440
23
votes
8
replies
28k
views
What is the difference between narrow peak, Broad peak and a gapped peak of a chip-seq experiment and is it okay to use all of these regions for dow…
peaks
broad
gapped
chip-seq
narrow
updated 20 months ago by
Ram
44k • written 8.6 years ago by
Saad Khan
▴ 440
1
vote
4
replies
2.2k
views
Can something like this be done in IGV or other better browsers
coverage
ggbio
exome
SNV
updated 20 months ago by
Ram
44k • written 8.6 years ago by
Saad Khan
▴ 440
0
votes
0
replies
1.8k
views
Contact residue map of mutated protein around active sites
pymol
chimera
active-site
contact-map
8.6 years ago by
Saad Khan
▴ 440
0
votes
2
replies
1.6k
views
Visualizing multiple average profiles
histones
profiles
average
updated 20 months ago by
Ram
44k • written 8.7 years ago by
Saad Khan
▴ 440
3
votes
6
replies
4.6k
views
Transcriptional repressors and transcriptional activators
transcription factors
chhip-seq
RNA-Seq
TF binding
updated 19 months ago by
Ram
44k • written 8.8 years ago by
Saad Khan
▴ 440
0
votes
2
replies
1.8k
views
orthologous transcription factors and their binding sites
orthologous-transcription-factors
binding-sites
updated 16 months ago by
Ram
44k • written 9.0 years ago by
Saad Khan
▴ 440
0
votes
1
reply
3.2k
views
How does vcf-stats give snp count
vcf
snp-count
updated 2.0 years ago by
Ram
44k • written 9.0 years ago by
Saad Khan
▴ 440
2
votes
2
replies
2.3k
views
Visualizing microRNA expression network
cytoscape
expression-network
microRNA
updated 15 months ago by
Ram
44k • written 9.0 years ago by
Saad Khan
▴ 440
4
votes
1
reply
2.3k
views
How to combine bisulfite sequencing data with Medip seq and/or MRE-seq
DNA methylation
bisulfite-sequencing
medipseq
updated 15 months ago by
Ram
44k • written 9.1 years ago by
Saad Khan
▴ 440
1
vote
1
reply
1.8k
views
Known transcription factor binding sites and enhancer locations in Pigs
TFBS
enhancer
updated 15 months ago by
Ram
44k • written 9.1 years ago by
Saad Khan
▴ 440
0
votes
1
reply
2.6k
views
How to compare multiple microarray samples of small RNA expression from myeloid tissue with small RNA-seq
myeloid
microRNA
small-RNA
cancer
updated 15 months ago by
Ram
44k • written 9.1 years ago by
Saad Khan
▴ 440
0
votes
3
replies
1.8k
views
Can anova analysis be done on one vs many microRNA count data
microrna
anova
cancer
updated 23 months ago by
Ram
44k • written 9.1 years ago by
Saad Khan
▴ 440
0
votes
1
reply
1.8k
views
smallRNA-seq data for normal bone marrow in Human
normal
small-RNA
bonemarrow
RNA-Seq
9.1 years ago by
Saad Khan
▴ 440
2
votes
2
replies
2.4k
views
Where can I download old NIH research proposals (Ro1 grant)
NIH
RO1
updated 9.1 years ago by
Sean Davis
27k • written 9.1 years ago by
Saad Khan
▴ 440
0
votes
3
replies
1.9k
views
What computational methods exist or have been used in order to study trans-acting elements in molecular biology.
trans-acting
genes
histones
updated 24 months ago by
Ram
44k • written 9.2 years ago by
Saad Khan
▴ 440
2
votes
8
replies
2.4k
views
Differential expression of microRNA with no replicates
RNA-Seq
small RNA
updated 2.0 years ago by
Ram
44k • written 9.2 years ago by
Saad Khan
▴ 440
9
votes
30
replies
11k
views
small RNA-seq pipelines
small-RNA-seq
pipelines
updated 2.0 years ago by
Ram
44k • written 9.3 years ago by
Saad Khan
▴ 440
0
votes
2
replies
2.2k
views
SRA file looks wierd after conversion to fastq
fastq
SRA
fastq-dump
updated 2.1 years ago by
Ram
44k • written 9.3 years ago by
Saad Khan
▴ 440
2
votes
3
replies
1.9k
views
Documenting all available data sets of histone modifications in GEO
GEO
Histones
SRA
e-utils
GEO parser
updated 2.1 years ago by
Ram
44k • written 9.3 years ago by
Saad Khan
▴ 440
0
votes
1
reply
2.1k
views
How much overlap to consider when annotating a region
bed
annotation
updated 2.1 years ago by
Ram
44k • written 9.5 years ago by
Saad Khan
▴ 440
1
vote
1
reply
2.9k
views
ggbio error when autoplot on PTPN11 gene
ggbio
tracks
plots
updated 2.4 years ago by
Ram
44k • written 9.7 years ago by
Saad Khan
▴ 440
0
votes
2
replies
2.4k
views
Quick way to find all the TFBS peak data for mouse and Human in GEO
peak
GEO
TFBS
ucsc
updated 2.3 years ago by
Ram
44k • written 9.5 years ago by
Saad Khan
▴ 440
0
votes
0
replies
2.0k
views
liftover one to one mappings
mapping
liftover
updated 2.2 years ago by
Ram
44k • written 9.5 years ago by
Saad Khan
▴ 440
0
votes
0
replies
2.0k
views
wig file change span from 150 to 300
span-size
wig
updated 2.3 years ago by
Ram
44k • written 9.5 years ago by
Saad Khan
▴ 440
0
votes
2
replies
2.2k
views
Using CEAS with canine methylation data
CEAS
dog
medip-seq
methylation
updated 2.4 years ago by
Ram
44k • written 9.7 years ago by
Saad Khan
▴ 440
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