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121,188 results • Page
2 of 2424
Sort: Rank
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Votes
Replies
0
votes
0
replies
176
views
IM-fusion data analysis
IM-fusion
4 days ago by
frarodmar17
• 0
0
votes
4
replies
342
views
error in reading codelink data
readcodelinkset
2 days ago by
nazaninhoseinkhan
▴ 530
0
votes
1
reply
247
views
DiffBind analysis with ENCODE data using R and .bed/.bam files
R
ChIP-seq
ENCODE
Diffbind
updated 4 days ago by
Aspire
▴ 380 • written 4 days ago by
stalo.lili
• 0
7
votes
5
replies
695
views
No variant in the Pseudoautosomal regions of gomad chrY ?
chrY
PAR
vcf
gnomad
Pseudoautosomal
updated 3 days ago by
cmdcolin
★ 4.2k • written 19 days ago by
Pierre Lindenbaum
166k
8
votes
6
replies
3.3k
views
News:
Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming Up
python
training
updated 4 days ago by
GenoMax
151k • written 12.1 years ago by
Mary
11k
1
vote
1
reply
293
views
Selecting clinical rows for repeated case IDs in TCGA-BRCA data
Clinical-Data
Breast-Cancer
TCGA
updated 4 days ago by
Zhenyu Zhang
★ 1.3k • written 7 days ago by
BhagyashreeWaghale
• 0
0
votes
2
replies
331
views
Kallisto to tximport to deseq2
enseml
deseq2
Kallisto
updated 5 days ago by
GenoMax
151k • written 5 days ago by
bioinfo
▴ 150
0
votes
0
replies
199
views
Tool for Estimation of Purity and Ploidy in Precancerous Lesions
CNV
purity
genome
ploidy
6 days ago by
ting
• 0
10
votes
8
replies
738
views
6 follow
Nextflow: split a FASTA file into 5 parts to enable parallel processing
nextflow
workflow
pipeline
6 days ago by
neng
▴ 50
0
votes
1
reply
262
views
What to choose as background in statistic test genetics
test
expression
gene
statistic
updated 5 days ago by
Dunois
★ 2.9k • written 6 days ago by
adigershon8897
• 0
5
votes
4
replies
499
views
differential exon usage from Salmon outputs
edgeR
diffSpliceDGE
DEU
salmon
updated 6 days ago by
Gordon Smyth
★ 8.1k • written 9 days ago by
n_navy
• 0
0
votes
0
replies
468
views
Multi-SNP Behavioral and Frequency Profile Inquiry: TPH2, GRM2, COMT, DRD2, HTR1A (Rare Interaction)
population-genetics
genetic-variation
epistasis
snp
gnomad
6 days ago by
SonicSoal
• 0
0
votes
0
replies
199
views
Rare variants association analysis (using WGS)
variant
GWAS
rare
WGS
6 days ago by
SeoG
• 0
0
votes
0
replies
203
views
Convert AnnData to Seurat (spatial transcriptomics, visium HD)
seurat
segmentation
anndata
visiumhd
updated 7 days ago by
GenoMax
151k • written 7 days ago by
npont
• 0
0
votes
0
replies
208
views
News:
Online course -Reproducibility in Bioinformatics - July 7–9
Singularity
Git
Docker
Snakemake
Nextflow
7 days ago by
Physalia-courses
★ 2.6k
1
vote
5
replies
475
views
RNA-Sequencing Analysis when control samples paired-end and tumour samples single-end
ENA
rna-sequencing
7 days ago by
h
• 0
0
votes
3
replies
357
views
STAR aligner - how is quality and correctness tested across builds/releases?
STAR
updated 7 days ago by
GenoMax
151k • written 7 days ago by
Arthur
• 0
1
vote
2
replies
343
views
Pathway enrichment analysis on time-series data by filtering out age comparisons
pea
go
rnaseq
time-series
7 days ago by
fullycratered
• 0
6
votes
8
replies
542
views
building snpeff database for plant
plant
updated 3 days ago by
lieven.sterck
15k • written 7 days ago by
analyst
▴ 60
1
vote
1
reply
250
views
How to find motif in specific region
motif
chip-seq
updated 7 days ago by
Alex Reynolds
36k • written 7 days ago by
zhang616123
• 0
0
votes
0
replies
230
views
How to interpret perplexing qcovhsp result in blastx
blastx
qcovhsp
blastn
7 days ago by
samuel.himes
• 0
0
votes
0
replies
195
views
Representation of GT:DS INFO tag for a missing marker in a VCF file
VCF
bcftools
7 days ago by
Mwangana
• 0
0
votes
0
replies
213
views
Best Practices for Integrating RNA-seq Time Series from Multiple Studies with Varying Protocols
differential-expression
meta-analysis
integration
RNA-seq
time-series
8 days ago by
enee
▴ 20
10
votes
9
replies
5.0k
views
bcftools query add header
bcftools
updated 8 days ago by
GenoMax
151k • written 3.1 years ago by
User000
▴ 750
0
votes
2
replies
388
views
Alternative to PASApipeline
transcriptomics
annotation
updated 7 days ago by
colindaven
7.4k • written 9 days ago by
lagartija
▴ 160
0
votes
0
replies
210
views
How to Get a Genetic Map, Given the Physical Position and Genotype Data of Markers
genetic-map
updated 8 days ago by
Ram
45k • written 8 days ago by
Daniyal
• 0
1
vote
7
replies
2.5k
views
vcftools --weir-fst-pop returns -nan
fst
vcftools
updated 8 days ago by
Michael
55k • written 2.4 years ago by
elizabeth
• 0
1
vote
3
replies
365
views
HISAT2 with Cleaned Data
HISAT2
RNASeq
updated 4 days ago by
lieven.sterck
15k • written 8 days ago by
Gordonz9494
▴ 10
4
votes
1
reply
295
views
Definitions for "differential expression" and "differential abundance" in RNA-seq?
rna-seq
deseq
abundance
differential-expression
updated 8 days ago by
Ram
45k • written 8 days ago by
tw_140
• 0
2
votes
5
replies
445
views
Efficiently find regions in bed file that are within start and end regions of another bed file.
intersect
bedtools
updated 7 days ago by
Alex Reynolds
36k • written 9 days ago by
rxs1018
• 0
2
votes
4
replies
379
views
16S Libraries With Non-Purified Short Fragments
Sequencing
16S
Libraries
Magnetic
Beads
8 days ago by
alenew.am
▴ 10
0
votes
1
reply
284
views
How to map polyA tails to barcodes in paired end reads for single cell RNA-seq
RNA-seq
cell
polyA
single
updated 9 days ago by
GenoMax
151k • written 9 days ago by
Ana
▴ 10
7
votes
6
replies
5.0k
views
Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
macs2
ChIP-Seq
ChromHMM
MACS2
CHROMHMM
updated 9 days ago by
luminea
▴ 10 • written 5.9 years ago by
m.sadman.sakib
▴ 120
4
votes
5
replies
544
views
Editing and Adding to a GTF file
Annotation
Gene-ID
GTF
updated 8 days ago by
Ram
45k • written 10 days ago by
Keem Uarren Eiryll
▴ 10
4
votes
2
replies
302
views
Averaging multiple IgG BAM files for use as a control in ChromHMM
ChromHMM
bam
averag
updated 9 days ago by
ATpoint
88k • written 9 days ago by
luminea
▴ 10
3
votes
3
replies
505
views
Deduplication rate of shotgun metagenomes using fastqc
metagenome
fastqc
shotgun
deduplication
updated 9 days ago by
colindaven
7.4k • written 14 days ago by
vikasmh111
• 0
0
votes
0
replies
205
views
News:
online course: Introduction to Genome Annotation
Gene-Prediction
Genome-Annotation
Gene-Models
9 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
1.4k
views
ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required. In metawrap - concoct binning module
concoct
metawrap
module
9 days ago by
shevch2009
• 0
6
votes
7
replies
549
views
Circular heatmap using circos.heatmap in R
R
circos
heatmap
circularheatmap
updated 8 days ago by
GenoMax
151k • written 9 days ago by
Yukta
• 0
0
votes
0
replies
228
views
Zebrafish phenotype ontology enrichment analyses
ontology
zebrafish
9 days ago by
Li
• 0
0
votes
2
replies
319
views
Sequence Duplication for Single-End 3RAD Data
duplication
reduced-representation
8 days ago by
Sarah
• 0
0
votes
0
replies
230
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg
cytoscape
9 days ago by
Adrian
• 0
1
vote
6
replies
1.2k
views
6 follow
Not retrieving Mitochondrial Genes in Single Cell analysis
single-cell
updated 9 days ago by
Ram
45k • written 10 months ago by
guioliveirareis
▴ 10
0
votes
0
replies
222
views
News:
Ancient Metagenomics course - online, May 27-29
ancient-metagenomics
aDNA
aMeta
10 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
276
views
Issues running scAPAtrap
scAPAtrap
polyA
scRNAseq
updated 10 days ago by
GenoMax
151k • written 10 days ago by
Ana
▴ 10
5
votes
3
replies
393
views
What are BED files?
BED
updated 9 days ago by
Alex Reynolds
36k • written 10 days ago by
Besoa
• 0
3
votes
8
replies
589
views
ggplot make boxplots more wide
ggplot2
r
10 days ago by
Nona
▴ 90
2
votes
1
reply
342
views
Minimum number of samples for multi-omics data integration
multi-omics
updated 10 days ago by
Ram
45k • written 10 days ago by
Tundup
▴ 10
1
vote
0
replies
266
views
News:
Workshop: Virtual Genome Annotation, May 27–29
GenomeAnnotation
workshop
UConn
10 days ago by
zsc25001
▴ 10
1
vote
1
reply
316
views
Assigning a string variable on Visual Studio using python
python
visual-studio
updated 10 days ago by
Ram
45k • written 10 days ago by
arthur_alexander83
• 0
121,188 results • Page
2 of 2424
Recent Votes
Answer: How to visualize Combat-seq corrected counts
Answer: How to visualize Combat-seq corrected counts
Comment: How to visualize Combat-seq corrected counts
Answer: Definitions for "differential expression" and "differential abundance" in RNA-se
Answer: Definitions for "differential expression" and "differential abundance" in RNA-se
Answer: Heatmap of a transformed deseq object with pheatmap
Answer: Pie Charts: to use or not to use
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Comment: How to visualize Combat-seq corrected counts
by
ybw8gh
• 0
Sorry, I accidentally used ComBat! ComBat-seq did not produce negative counts. Thanks for all the help!
Answer: Trimmomatic command
by
swbarnes2
14k
Keep in mind for RNASeq 1) if the library was done properly, it's very unlikely you have many fragments shorter than your read length. …
Comment: Setaria Pan-Genome Variation: Unraveling the Story of Domestication
by
cmdcolin
★ 4.2k
>de novo assembled 110 reference-grade genomes for cultivated Setaria accessions this type of routine de novo assembly of genomes is aweso…
Comment: Facing issue with output of nextflow pipeline
by
ATpoint
88k
It looks hacky. Maybe it "works" but should not be taken as inspiration I guess. Are you sure output could be redicted to other processed l…
Comment: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci
by
GenoMax
151k
Have you considered the possibility that if no strains of Acinetobacter guillouiae available in NCBI show presence of nitrogen fixing genes…
Answer: Facing issue with output of nextflow pipeline
by
neng
▴ 50
This is a common issue that many learners encounter when working with Nextflow output management. 1. Use publishDir("${params.outdir}/..…
Comment: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci
by
Nafi
• 0
Yes, I have tested all of them. I guess NCBI does not have this particular strain.
Answer: Pie Charts: to use or not to use
by
Joe
22k
As with any visualisation method, there is a time and a place for them. They are often misused, or used when a different method would be be…
Answer: Pie Charts: to use or not to use
by
Bastien Hervé
6.3k
Your first paragraph is answering the latter and as said in the second paragraph, one cannot force people not to use it. It is like RPKM/F…
Comment: Target prediction
by
dthorbur
★ 3.0k
I'm unfamiliar with the representation of phytochemicals in either database, so can't answer for certain, but generally I would say both da…
Answer: Minimum Number of Cells for Downstream Analysis after subsetting a particular ce
by
ATpoint
88k
There is no answer to this. Some people will say 10, other 3, others 500. Generally, since single-cell is noisy and has dropouts, even for …
Answer: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci
by
Mensur Dlakic
★ 29k
The specific strain described in that paper (*Acinetobacter guillouiae* EU-B2RT.R1) doesn't seem to be available in NCBI. It could be as si…
Comment: Heatmap of a transformed deseq object with pheatmap
by
GenoMax
151k
Please use `ADD REPLY/ADD COMMENT` when responding to existing posts. `ADD ANSWER` is only for new answers to original question.
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
• 0
...I decided to try 'ComplexHeatmap' : ```r ha = HeatmapAnnotation(df = annot_col, which="column",show_annotation_name = FALSE,show_legend=…
Comment: PRS result interpretation
by
trkfs
▴ 10
Much thanks for your reply. If I could ask - what would be the best way or what kind of data is typically needed to obtain a PRS score that…
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