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1,000 results • Page
1 of 20
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0
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1
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How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
NGS
bcftools
vcf
phase
just now by
zhangfish
▴ 40
0
votes
0
replies
5
views
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
11 minutes ago by
Joana
• 0
0
votes
0
replies
7
views
Snakemake vs Nextflow Upcoming bioinformatics Project
Bioinformatics
Programming
Masters
19 minutes ago by
rackbersingh
• 0
0
votes
0
replies
24
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
43 minutes ago by
firestar
★ 1.5k
0
votes
2
replies
33
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
15 minutes ago by
TJay
• 0
0
votes
0
replies
20
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
1 hour ago by
predeus
★ 1.8k
0
votes
0
replies
28
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
1 hour ago by
ucbtep
▴ 20
2
votes
5
replies
91
views
GATK GenotypeGVCFs explain
calling
gatk
variant
GenotypeGVCFs
updated 1 hour ago by
Pierre Lindenbaum
153k • written 3 hours ago by
Sarah
▴ 30
0
votes
0
replies
62
views
Dnaplotter
Artemis
4 hours ago by
prs
• 0
1
vote
1
reply
98
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 3 hours ago by
Basti
★ 1.4k • written 5 hours ago by
Stefanus C.B.
• 0
0
votes
1
reply
101
views
mrbayes segmentation fault
mrbayes
segmentation
fault
updated 5 hours ago by
Mensur Dlakic
★ 23k • written 8 hours ago by
dgrace999
• 0
0
votes
0
replies
72
views
Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot
TSS
GRanges
EnrichedPlot
promoters
GenomicRanges
9 hours ago by
melissachuaphd
• 0
0
votes
0
replies
76
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
13 hours ago by
William
▴ 10
0
votes
0
replies
101
views
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
GSVA
limma
R
14 hours ago by
Tadeoye
▴ 30
0
votes
0
replies
93
views
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
isoforms
Salmon
RNA-seq
CD45
14 hours ago by
eager_underdog
• 0
0
votes
5
replies
208
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 30 minutes ago by
GenoMax
126k • written 14 hours ago by
O.rka
▴ 650
0
votes
2
replies
153
views
Processing fastqs generated by inDrop protocol
single-cell
rna-seq
indrop
updated 13 hours ago by
Ram
38k • written 16 hours ago by
bobbybobbobbo
• 0
1
vote
3
replies
200
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 14 hours ago by
GenoMax
126k • written 17 hours ago by
Pegasus
▴ 80
0
votes
1
reply
119
views
Circos plot
circos
updated 3 hours ago by
Fabio Marroni
★ 3.0k • written 17 hours ago by
prs
• 0
0
votes
1
reply
97
views
mpileup2sync
mpileup2sync
population2
updated 16 hours ago by
Ram
38k • written 17 hours ago by
Hayler Edu
▴ 30
0
votes
0
replies
74
views
Number of gigabases necesary for Iso-seq-PacBio
Iso-seq
RNA-Seq
Alternative-Splicing
PacBio
updated 17 hours ago by
Ram
38k • written 18 hours ago by
Jesús M
• 0
0
votes
2
replies
127
views
Problem with blasting UNMAPPED RNA-seq paired end reads in Jaculus jaculus
RNAseq
jaculus
unmapped
reads
18 hours ago by
barbarainb
• 0
0
votes
0
replies
59
views
PGx question regarding RSIDs with more than one variant associated with it
pharmacogenomics
rsid
pgx
19 hours ago by
Roy
▴ 10
0
votes
0
replies
85
views
Converting Abricate output (.tsv) to gff3 format
gff3
convert
tsv
Abricate
22 hours ago by
ghataksnd
▴ 10
0
votes
0
replies
94
views
samtools mpileup - bases string explanation
samtools
mpileup
23 hours ago by
igorm
▴ 20
0
votes
3
replies
207
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 16 hours ago by
Ram
38k • written 1 day ago by
VANSHIKA
• 0
0
votes
2
replies
164
views
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
vcf.gz
UnicodeDecodeError
ancIBD
1 day ago by
wangjincheng
• 0
0
votes
1
reply
178
views
Error while running Virusfinder
Virusfinder
updated 17 hours ago by
Ram
38k • written 1 day ago by
DC
• 0
0
votes
0
replies
125
views
Fine mapping with GWAS
PAINTOR
GWAS
FINE-MAP
POST-GWAS
updated 1 day ago by
Nicolas Rosewick
10k • written 1 day ago by
Swati
• 0
0
votes
0
replies
120
views
How would I assess evolutionary estimates between duplicated vs. non-duplicated genes in PAML?
PAML
1 day ago by
codoncity
• 0
1
vote
3
replies
249
views
FeatureCounts >edgeR > GO
RNA-SEQ
updated 3 hours ago by
Basti
★ 1.4k • written 1 day ago by
Pegasus
▴ 80
1
vote
2
replies
231
views
Handling single-sample VCF after haplotypecaller
VCF
1 day ago by
Y.H.P
• 0
0
votes
0
replies
139
views
MethylR on bam files Gives Error
MethylR
bismark
1 day ago by
anasjamshed
▴ 120
0
votes
0
replies
149
views
pyscenic
pyscenic
scenic
1 day ago by
Andy
▴ 30
1
vote
1
reply
219
views
just one plot appears in the shiny application not all
plot
source
shiny
code
updated 1 day ago by
bkleiboeker
▴ 320 • written 1 day ago by
mrashad
▴ 60
0
votes
1
reply
210
views
Circos plot using vcf : Mutect2 MultiSample VCF out file
Mutect2
vcf
updated 16 hours ago by
Ram
38k • written 2 days ago by
m. bioinfo
• 0
0
votes
0
replies
151
views
Downsample process in ActiveRegion determination (HaplotypeCaller and Mutect2)
Downsample
Mutect2
HaplotypeCaller
2 days ago by
yxwucq
• 0
0
votes
0
replies
216
views
Simes method
simes
method
SNP
R
1 day ago by
Eliza
▴ 10
0
votes
2
replies
290
views
Post-Imputation QC Problem
Imputation
18 hours ago by
Jesse
• 0
0
votes
1
reply
227
views
Conformational antigens
Immunoinformatics
updated 3 days ago by
Ram
38k • written 3 days ago by
Mohamed
• 0
0
votes
2
replies
310
views
best practice to choose AF threshold based on population number
VCF
AF
allele-frequency
3 days ago by
prasundutta87
▴ 650
2
votes
4
replies
466
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
1 day ago by
e.r.zakiev
▴ 30
0
votes
0
replies
177
views
selection of 2 by 2 Chi-square Test
statistics
Chi-square
updated 3 days ago by
Ram
38k • written 3 days ago by
Binghong
▴ 20
0
votes
0
replies
180
views
Check most expressed isoform of mouse gene in specific tissue
FANTOM
gene-expression
MGI
mouse
updated 3 days ago by
Ram
38k • written 3 days ago by
gspirito
▴ 10
1
vote
0
replies
176
views
gseKEGG with streptomyces coelicolor - No gene can be mapped
streptomyces
KEGG
clusterProfiler
4 days ago by
r.evans2
▴ 10
0
votes
0
replies
241
views
Power calculations for the detection of differentially expressed genes in pseudobulk scRNA-seq data
scRNA-seq
pseudobulk
power
RNA-seq
updated 3 days ago by
Ram
38k • written 4 days ago by
Ali
• 0
2
votes
8
replies
460
views
Depth of Coverage in Mitochondrial Genome with Samtools
samtools
depth-of-coverage
Mitochondrial-genome
2 days ago by
Lida
• 0
0
votes
1
reply
204
views
Genes near SNP within certain window frame and distance
bedops
bedtools
updated 3 days ago by
Ram
38k • written 4 days ago by
waqaskhokhar999
▴ 150
0
votes
0
replies
190
views
95% CI for AUC in R
AUC
R
4 days ago by
dhananya
• 0
0
votes
1
reply
232
views
comparison between STARsolo and cellranger
STARsolo
cellranger
updated 4 days ago by
GenoMax
126k • written 4 days ago by
dalibenam64
• 0
1,000 results • Page
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Recent Votes
Heatmaps in R
Answer: Extract Sub_Tree From Big Phylogeny
How to pair TCGA bam files with no properly paired reads?
How to pair TCGA bam files with no properly paired reads?
Answer: How to implement this two-stage one-to-many workflow using WDL?
Answer: How to implement this two-stage one-to-many workflow using WDL?
Answer: How to implement this two-stage one-to-many workflow using WDL?
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126k
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★ 1.8k
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Recent Replies
Comment: Plot heatmap using row_splitting but splitting should based on a column in data
by
TJay
• 0
Any guidance to make annotation object?
Comment: Plot heatmap using row_splitting but splitting should based on a column in data
by
rpolicastro
11k
Instead of splitting your dataset you want to make an annotation object via `rowAnnotation` and then pass it to the `left_annotation` argum…
Comment: How can I determine the number of detected genes and detected transcripts/isofor
by
GenoMax
126k
If this is single cell data then this is likely because of the 3' end detection bias. In general you are also detecting less genes because …
Comment: gene filtering for agilent microarray using Limma
by
Di Wu
• 0
Dear Prof. Kevin Blighe, many thanks for your quick reply. About the `correlation` value, I used the following code for getting the value. …
Comment: GATK GenotypeGVCFs explain
by
Pierre Lindenbaum
153k
https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists
Comment: GATK GenotypeGVCFs explain
by
Sarah
▴ 30
thank you
Comment: GATK GenotypeGVCFs explain
by
raphael.B
▴ 270
It limits the operation to some genomic regions given as parameter
Comment: GATK GenotypeGVCFs explain
by
Sarah
▴ 30
what does the option L
Comment: GATK GenotypeGVCFs explain
by
Pierre Lindenbaum
153k
GenotypeGVCFs takes a set of GVCF files called with HaplotyperCaler and output a VCF file.
Answer: TCGA Methylation Data and Gene Mapping
by
Basti
★ 1.4k
CpGs may be annotated to more than >1 gene simply because gene regions overlap on the genome. If you want to associate each gene to a me…
Comment: Circos plot
by
Fabio Marroni
★ 3.0k
Please give a look to [this post][1] for increasing the probability to get an answer. If I may add some needed info: 1. What exactly do y…
Comment: Trying to install Roary with Conda results in error message
by
tobiwan
▴ 10
Wow, thank you so much for your explanation! My conda channel is indeed set to strict priority. Should packages with different dependencie…
Comment: FeatureCounts >edgeR > GO
by
Basti
★ 1.4k
You can use BioMart to convert your "gene-IDs" to gene symbols, but you need to specify from which database your gene identifiers come from
Comment: How to create GO Bar Plot using data obtained from DAVID Functional Enrichment A
by
Basti
★ 1.4k
If you search "DAVID dotplot" on this forum, you have many answers to your question. Note that you can also perform DAVID Functional Enrich…
Answer: How to implement this two-stage one-to-many workflow using WDL?
by
Pierre Lindenbaum
153k
nottested, something like: ``` version 1.0 workflow BIOSTAR { call FIRST { } scatter (F in FIRST.each_F)…
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