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122,010 results • Page
283 of 2441
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
778
views
Plot in R: Presence of bacteria type A vs bacteria type B in different groups
boxplot
phyloseq
plot
abundance
ggplot2
R
updated 2.6 years ago by
Basti
★ 2.1k • written 2.6 years ago by
flourde
• 0
3
votes
1
reply
1.1k
views
Fastqc lsequence duplication and per base sequence content failed
RNA-seq
fastqc
updated 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
waqaskhokhar999
▴ 160
3
votes
12
replies
2.6k
views
prefix extraction and preparation for mapping and variant calling
bash
updated 2.6 years ago by
Joe
22k • written 2.6 years ago by
Human
• 0
4
votes
4
replies
7.0k
views
Nextflow memory issues custom config -c
nextflow
updated 2.6 years ago by
ATpoint
89k • written 3.8 years ago by
louisber2765
• 0
2
votes
3
replies
1.3k
views
wrong quality plots in fastqc output
samtools
fastqc
fastq
wgsim
updated 2.3 years ago by
Ram
45k • written 2.6 years ago by
poecile.pal
▴ 50
1
vote
5
replies
1.7k
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 2.6 years ago by
Trivas
★ 1.9k • written 2.6 years ago by
TJay
• 0
1
vote
1
reply
729
views
Why GATK is slow with haplotypecalling
GATK
HaplotypeCalling
updated 2.6 years ago by
Pierre Lindenbaum
166k • written 2.6 years ago by
rj.rezwan
▴ 20
0
votes
0
replies
701
views
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
vcf
bcftools
shapeit2
phase
NGS
updated 2.3 years ago by
Ram
45k • written 2.6 years ago by
octpus616
▴ 120
0
votes
0
replies
802
views
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
2.6 years ago by
Joana
• 0
0
votes
0
replies
1.1k
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
2.6 years ago by
firestar
★ 1.7k
0
votes
0
replies
642
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
2.6 years ago by
predeus
★ 2.1k
0
votes
0
replies
606
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
2.6 years ago by
Elizabeth
▴ 20
3
votes
1
reply
1.0k
views
TCGA Methylation Data and Gene Mapping
Methylation
Cancer
TCGA
updated 2.6 years ago by
Basti
★ 2.1k • written 2.6 years ago by
James
▴ 30
1
vote
2
replies
1.9k
views
Databases to check variant pathogenicity
WholeExomeSequencing
updated 2.6 years ago by
AtenaLia
▴ 50 • written 3.7 years ago by
Fatemeh Nabizadeh
▴ 10
2
votes
1
reply
1.4k
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 2.6 years ago by
Basti
★ 2.1k • written 2.6 years ago by
Stefanus C.B.
• 0
0
votes
2
replies
1.4k
views
mrbayes segmentation fault
mrbayes
segmentation
fault
2.6 years ago by
dgrace999
• 0
0
votes
0
replies
534
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
2.6 years ago by
William
▴ 20
0
votes
0
replies
578
views
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
GSVA
limma
R
2.6 years ago by
Tadeoye
▴ 30
1
vote
2
replies
1.2k
views
How to adjust for multiple batches using Combat-Seq
ComBat
RNA-seq
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
sabriledesma13
• 0
0
votes
0
replies
528
views
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
isoforms
Salmon
RNA-seq
CD45
2.6 years ago by
eager_underdog
• 0
0
votes
5
replies
1.5k
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 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
O.rka
▴ 750
0
votes
2
replies
1.1k
views
Processing fastqs generated by inDrop protocol
single-cell
rna-seq
indrop
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
bobbybobbobbo
• 0
1
vote
3
replies
1.5k
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 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
Pegasus
▴ 130
0
votes
1
reply
774
views
mpileup2sync
mpileup2sync
population2
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
Hayler Edu
▴ 40
0
votes
1
reply
2.9k
views
Blog:
list of old gene name in C. elegans
c.elegans
gene
wormbase
updated 2.6 years ago by
geneontologyhelp
▴ 470 • written 10.7 years ago by
firoz.imtech
▴ 50
3
votes
6
replies
1.9k
views
Pig Reference Genome
Genome
updated 2.6 years ago by
Joe
22k • written 2.6 years ago by
anasjamshed
▴ 140
0
votes
0
replies
528
views
Number of gigabases necesary for Iso-seq-PacBio
Iso-seq
RNA-Seq
Alternative-Splicing
PacBio
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
Jesús M
• 0
0
votes
4
replies
1.7k
views
how to create interacting Hi-C peaks
chromatin
interaction
gene
Hi-C
2.6 years ago by
rheab1230
▴ 150
0
votes
2
replies
1.7k
views
GSVA scores - positive and negative values - normalization prior to running PCA
clr
normalization
GSVA
scale
2.6 years ago by
Bianca
▴ 20
0
votes
2
replies
930
views
Problem with blasting UNMAPPED RNA-seq paired end reads in Jaculus jaculus
RNAseq
jaculus
unmapped
reads
2.6 years ago by
barbarainb
• 0
0
votes
0
replies
492
views
PGx question regarding RSIDs with more than one variant associated with it
pharmacogenomics
rsid
pgx
2.6 years ago by
Roy
▴ 20
0
votes
2
replies
1.2k
views
How to calculate the Z value of infernal cmscan?
cmscan
ncRNA
infernal
updated 2.6 years ago by
Dunois
★ 2.9k • written 2.6 years ago by
shelvenlone
• 0
5
votes
5
replies
2.0k
views
samtools idxstats not removing ChrM
samtools
ChIP-seq
updated 2.3 years ago by
Ram
45k • written 2.6 years ago by
Jen
▴ 100
2
votes
3
replies
1.7k
views
how to get pfam id of proteins belonging to a particular family along with sequences in that family?
pfam
protein
id
interpro
sequence
2.6 years ago by
max
• 0
0
votes
0
replies
917
views
Converting Abricate output (.tsv) to gff3 format
Abricate
gff3
updated 2.3 years ago by
Ram
45k • written 2.6 years ago by
ghataksnd
▴ 20
0
votes
0
replies
527
views
samtools mpileup - bases string explanation
samtools
mpileup
2.6 years ago by
igorm
▴ 20
0
votes
3
replies
1.5k
views
Practical Haplotype Graph -- Pathing Error
PHG
updated 2.6 years ago by
lcj34
▴ 420 • written 2.6 years ago by
wcs98
• 0
0
votes
3
replies
1.2k
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
VANSHIKA
• 0
7
votes
7
replies
4.8k
views
Trying to install Roary with Conda results in error message
roary
conda
2.6 years ago by
tobiwan
▴ 10
0
votes
2
replies
1.9k
views
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
vcf.gz
UnicodeDecodeError
ancIBD
2.6 years ago by
wangjincheng
• 0
3
votes
2
replies
1.5k
views
What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k_v1 in biomart?
genetics
biomaRt
gene
updated 4 weeks ago by
Jacob
• 0 • written 2.6 years ago by
solarchan7
• 0
0
votes
1
reply
621
views
Error while running Virusfinder
Virusfinder
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
DC
• 0
17
votes
8
replies
2.8k
views
Where do find virulence gene information in a gff/gtf file?
microbial
genomics
gff
annotation
gtf
2.6 years ago by
sovrappensiero
▴ 100
11
votes
8
replies
3.0k
views
6 follow
split fasta file to train deep learning model
fasta
split
bash
R
updated 2.5 years ago by
shenwei356
8.7k • written 2.6 years ago by
pinheirofabiano
▴ 130
0
votes
0
replies
543
views
Fine mapping with GWAS
PAINTOR
GWAS
FINE-MAP
POST-GWAS
updated 2.6 years ago by
Nicolas Rosewick
11k • written 2.6 years ago by
Swati
• 0
0
votes
2
replies
2.1k
views
GIAB Truth Set
GIAB
2.6 years ago by
samuel
▴ 260
0
votes
0
replies
479
views
How would I assess evolutionary estimates between duplicated vs. non-duplicated genes in PAML?
PAML
2.6 years ago by
codoncity
• 0
2
votes
2
replies
1.3k
views
FastQ file not recognized by hisat2 allignment
hisat2
rnaseq
rna-seq
nextflow
updated 2.6 years ago by
Maxime Garcia
▴ 410 • written 2.6 years ago by
selenaajohn
• 0
2
votes
4
replies
1.7k
views
FeatureCounts >edgeR > GO
RNA-SEQ
2.5 years ago by
Pegasus
▴ 130
2
votes
2
replies
5.3k
views
BWA alignment score calculation
score
SAM
BWA
alignment
updated 2.6 years ago by
kmzhou4
• 0 • written 4.3 years ago by
Donovan
▴ 20
122,010 results • Page
283 of 2441
Recent Votes
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Answer: DESeq2 on metagenome KO counts
Comment: GUI commercial software for 10x single cell gene expression analysis
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If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
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89k
This statement makes zero sense in response to what I wrote.
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I focused on the fact that DESeq2 models overdispersion, but overlooked its implicit assumption: normalisation works when the main source o…
Comment: DESeq2 on metagenome KO counts
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Thank you very much. I mistakenly drew a superficial analogy. I equated KO counters with gene counters.
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Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
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3.9k
I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions: 1. All genes with t…
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