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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
5
replies
306
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 2 days ago by
Trivas
▴ 690 • written 2 days ago by
TJay
• 0
1
vote
1
reply
137
views
Why GATK is slow with haplotypecalling
GATK
HaplotypeCalling
updated 2 days ago by
Pierre Lindenbaum
153k • written 2 days ago by
rj.rezwan
• 0
0
votes
0
replies
99
views
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
NGS
bcftools
vcf
phase
2 days ago by
zhangfish
▴ 40
0
votes
0
replies
83
views
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
2 days ago by
Joana
• 0
0
votes
0
replies
120
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
2 days ago by
firestar
★ 1.5k
0
votes
0
replies
108
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
2 days ago by
predeus
★ 1.8k
0
votes
0
replies
110
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
2 days ago by
ucbtep
▴ 20
0
votes
0
replies
135
views
Dnaplotter
Artemis
2 days ago by
prs
• 0
2
votes
1
reply
201
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 2 days ago by
Basti
★ 1.4k • written 2 days ago by
Stefanus C.B.
• 0
0
votes
2
replies
198
views
mrbayes segmentation fault
mrbayes
segmentation
fault
1 day ago by
dgrace999
• 0
0
votes
0
replies
126
views
Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot
TSS
GRanges
EnrichedPlot
promoters
GenomicRanges
2 days ago by
melissachuaphd
• 0
0
votes
0
replies
117
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
2 days ago by
William
▴ 10
0
votes
0
replies
145
views
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
GSVA
limma
R
2 days ago by
Tadeoye
▴ 30
0
votes
0
replies
126
views
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
isoforms
Salmon
RNA-seq
CD45
2 days ago by
eager_underdog
• 0
0
votes
5
replies
310
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq
scRNA-seq
single-cell
genomics
ngs
updated 2 days ago by
GenoMax
127k • written 2 days ago by
O.rka
▴ 650
0
votes
2
replies
202
views
Processing fastqs generated by inDrop protocol
single-cell
rna-seq
indrop
updated 2 days ago by
Ram
38k • written 3 days ago by
bobbybobbobbo
• 0
1
vote
3
replies
262
views
How to extract/find the actual names of the gene_IDs if they are not fully presented in gtf.file, and link them to the Count.matrix
featureCounts
gtf
RNA-Seq
updated 2 days ago by
GenoMax
127k • written 3 days ago by
Pegasus
▴ 80
0
votes
1
reply
185
views
Circos plot
circos
updated 2 days ago by
Fabio Marroni
★ 3.0k • written 3 days ago by
prs
• 0
0
votes
1
reply
121
views
mpileup2sync
mpileup2sync
population2
updated 3 days ago by
Ram
38k • written 3 days ago by
Hayler Edu
▴ 30
0
votes
0
replies
92
views
Number of gigabases necesary for Iso-seq-PacBio
Iso-seq
RNA-Seq
Alternative-Splicing
PacBio
updated 3 days ago by
Ram
38k • written 3 days ago by
Jesús M
• 0
0
votes
2
replies
149
views
Problem with blasting UNMAPPED RNA-seq paired end reads in Jaculus jaculus
RNAseq
jaculus
unmapped
reads
3 days ago by
barbarainb
• 0
0
votes
0
replies
76
views
PGx question regarding RSIDs with more than one variant associated with it
pharmacogenomics
rsid
pgx
3 days ago by
Roy
▴ 10
0
votes
0
replies
100
views
Converting Abricate output (.tsv) to gff3 format
gff3
convert
tsv
Abricate
3 days ago by
ghataksnd
▴ 10
0
votes
0
replies
111
views
samtools mpileup - bases string explanation
samtools
mpileup
3 days ago by
igorm
▴ 20
0
votes
3
replies
229
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 3 days ago by
Ram
38k • written 3 days ago by
VANSHIKA
• 0
0
votes
2
replies
193
views
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
vcf.gz
UnicodeDecodeError
ancIBD
3 days ago by
wangjincheng
• 0
0
votes
1
reply
198
views
Error while running Virusfinder
Virusfinder
updated 3 days ago by
Ram
38k • written 3 days ago by
DC
• 0
0
votes
0
replies
143
views
Fine mapping with GWAS
PAINTOR
GWAS
FINE-MAP
POST-GWAS
updated 3 days ago by
Nicolas Rosewick
10k • written 3 days ago by
Swati
• 0
0
votes
0
replies
131
views
How would I assess evolutionary estimates between duplicated vs. non-duplicated genes in PAML?
PAML
3 days ago by
codoncity
• 0
1
vote
3
replies
296
views
FeatureCounts >edgeR > GO
RNA-SEQ
updated 2 days ago by
Basti
★ 1.4k • written 3 days ago by
Pegasus
▴ 80
1
vote
2
replies
251
views
Handling single-sample VCF after haplotypecaller
VCF
3 days ago by
Y.H.P
• 0
0
votes
0
replies
145
views
MethylR on bam files Gives Error
MethylR
bismark
4 days ago by
anasjamshed
▴ 120
0
votes
1
reply
178
views
pyscenic
pyscenic
scenic
1 day ago by
Andy
▴ 30
1
vote
1
reply
228
views
just one plot appears in the shiny application not all
plot
source
shiny
code
updated 3 days ago by
bkleiboeker
▴ 320 • written 4 days ago by
mrashad
▴ 60
0
votes
0
replies
155
views
Downsample process in ActiveRegion determination (HaplotypeCaller and Mutect2)
Downsample
Mutect2
HaplotypeCaller
4 days ago by
yxwucq
• 0
0
votes
0
replies
226
views
Simes method
simes
method
SNP
R
3 days ago by
Eliza
▴ 10
0
votes
2
replies
314
views
Post-Imputation QC Problem
Imputation
3 days ago by
Jesse
• 0
0
votes
1
reply
239
views
Conformational antigens
Immunoinformatics
updated 6 days ago by
Ram
38k • written 6 days ago by
Mohamed
• 0
0
votes
2
replies
317
views
best practice to choose AF threshold based on population number
VCF
AF
allele-frequency
5 days ago by
prasundutta87
▴ 650
2
votes
5
replies
536
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 2 days ago by
igor
13k • written 6 days ago by
e.r.zakiev
▴ 30
0
votes
0
replies
187
views
selection of 2 by 2 Chi-square Test
statistics
Chi-square
updated 6 days ago by
Ram
38k • written 6 days ago by
Binghong
▴ 20
0
votes
0
replies
186
views
Check most expressed isoform of mouse gene in specific tissue
FANTOM
gene-expression
MGI
mouse
updated 6 days ago by
Ram
38k • written 6 days ago by
gspirito
▴ 10
1
vote
0
replies
181
views
gseKEGG with streptomyces coelicolor - No gene can be mapped
streptomyces
KEGG
clusterProfiler
6 days ago by
r.evans2
▴ 10
0
votes
0
replies
251
views
Power calculations for the detection of differentially expressed genes in pseudobulk scRNA-seq data
scRNA-seq
pseudobulk
power
RNA-seq
updated 6 days ago by
Ram
38k • written 6 days ago by
Ali
• 0
2
votes
8
replies
488
views
Depth of Coverage in Mitochondrial Genome with Samtools
samtools
depth-of-coverage
Mitochondrial-genome
4 days ago by
Lida
• 0
0
votes
1
reply
210
views
Genes near SNP within certain window frame and distance
bedops
bedtools
updated 6 days ago by
Ram
38k • written 6 days ago by
waqaskhokhar999
▴ 150
0
votes
0
replies
195
views
95% CI for AUC in R
AUC
R
6 days ago by
dhananya
• 0
0
votes
1
reply
256
views
comparison between STARsolo and cellranger
STARsolo
cellranger
updated 6 days ago by
GenoMax
127k • written 6 days ago by
dalibenam64
• 0
0
votes
1
reply
192
views
building model with lectin array data and patient data
lectin
model
updated 6 days ago by
ATpoint
70k • written 6 days ago by
dharmini1998
• 0
1
vote
1
reply
215
views
What's the correct way to map to hg38 with alternative contigs?
NGS
bwa
updated 6 days ago by
ATpoint
70k • written 6 days ago by
Belanov
▴ 10
1,000 results • Page
2 of 20
Recent Votes
Comment: bioinformatics problems solved by graphs data structure
Comment: bioinformatics problems solved by graphs data structure
Answer: How to analize multiple letters codes in COG IDs?
Answer: PCA in gene expression
Answer: PCA in gene expression
Comment: Enrichment analysis based on kegg for zebrafish
Question on number of possible alignments
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Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
et mon français est assez bien pour comprendre ce que tu as écrit la ;-)
Comment: How to analize multiple letters codes in COG IDs?
by
Constanza
• 0
Thanks for answering so fast, it was very helpful. I shouldn't pay much attention to if COGs are separated by a comma or not then. As long…
Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
well, because this is not you guys' private forum, there are other people participating (not native french speaking) , just to give a reaso…
Answer: How to get gene from PSIBLAST resuts
by
lieven.sterck
14k
what you likely will need to do: 1. get the ID of the protein that you are interested in (out of result from PSIBLAST) 2. lookup that ID…
Answer: How to analize multiple letters codes in COG IDs?
by
Mensur Dlakic
★ 23k
The meaning of individual letters is described in a well-known COG functional code: https://ecoliwiki.org/colipedia/index.php/Clusters_o…
Comment: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
The organism is mice.
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file?
by
Pierre Lindenbaum
153k
BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gperte…
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs?
by
Darked89
4.2k
You may try to check what happened with DEGs obtained using the 300 fragments assembly by getting the sequences of these genes and comparin…
Comment: ExomeDepth installation error
by
Medha
• 0
Thanks, that did work. Also in next steps, there are some arguments like bam.files, I was wondering do we require to have multiple bam fil…
Comment: ExomeDepth installation error
by
jared.andrews07
★ 14k
No idea, I don't use databricks. I'd read the docs, find a local expert to help you out, or contact their support, likely in that order.
Comment: ExomeDepth installation error
by
Medha
• 0
Hi @jaredandrews07 thanks for reverting back. I am new to R and just want to make sure ExomeDepth is working for the first time. For the Rs…
Comment: Embedded stop codon in translated nucleotide sequences in DAMBE
by
Mensur Dlakic
★ 23k
It is not obvious to me what exact steps you did here, but here is what I do know: there will always be stop codons even in open reading fr…
Comment: Error with a function in ATAC-seq analysis
by
Chris
▴ 70
So you skip the GRanges()? Yes, no error anymore but I am not sure if that causes changing in downstream analysis.
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
by
jv
★ 1.0k
`stringr::str_remove` can remove " - Mus musculus (house mouse)" from the pathway names which are stored under `KEGGPATHID2NAME$to` in your…
Comment: Error with a function in ATAC-seq analysis
by
jv
★ 1.0k
run `union` on the data frames
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