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175 results • Page
3 of 4
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Replies
0
votes
1
reply
456
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 17 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
502
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 2 days ago by
Ram
43k • written 2 days ago by
Dr Huma Naz
• 0
0
votes
1
reply
184
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 1 day ago by
GenoMax
142k • written 1 day ago by
mgranada3
▴ 30
0
votes
1
reply
115
views
RNA-seq data for deep learning classification
rna-seq
updated 16 hours ago by
dsull
★ 5.9k • written 18 hours ago by
Yuju
• 0
0
votes
1
reply
111
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 15 hours ago by
Ram
43k • written 1 day ago by
nithya
• 0
0
votes
1
reply
4
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated just now by
ATpoint
82k • written 3 minutes ago by
adi.gershon1
• 0
0
votes
1
reply
206
views
Finding batch and outlayers
Pca
updated 4 days ago by
christopher medway
▴ 450 • written 4 days ago by
Tigran
• 0
0
votes
1
reply
95
views
Provean help
variant
Provean
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 18 hours ago by
Arun Sai Kumar
• 0
0
votes
1
reply
566
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 1 day ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
1
reply
142
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 4 days ago by
i.sudbery
19k • written 4 days ago by
DOBI
• 0
0
votes
1
reply
98
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 13 hours ago by
anovak
▴ 120 • written 17 hours ago by
Hang
• 0
0
votes
1
reply
330
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by
Jesse
▴ 740 • written 13 days ago by
yifangt86
▴ 60
0
votes
1
reply
253
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 1 day ago by
Scooter
▴ 280 • written 7 days ago by
avocado123
• 0
0
votes
1
reply
169
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Edmond
• 0
0
votes
1
reply
168
views
Downloading full alignments from Pfam
pfam
updated 4 days ago by
GenoMax
142k • written 4 days ago by
bef1
• 0
0
votes
1
reply
747
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 4 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
0
votes
1
reply
125
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 6 hours ago by
Chris Dean
▴ 390 • written 15 hours ago by
sovrappensiero
▴ 90
0
votes
1
reply
157
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
1
reply
526
views
HOMER on AWS
HOMER
updated 6 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
1
reply
178
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
1
vote
1
reply
163
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
2 days ago by
heelpPlease
• 0
0
votes
1
reply
176
views
Deseq2
Deseq2
updated 3 days ago by
Jack Tierney
▴ 360 • written 3 days ago by
Sudip
• 0
0
votes
1
reply
197
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
J
• 0
0
votes
1
reply
273
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
3 days ago by
David Langenberger
11k
1
vote
1
reply
210
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 3 days ago by
Michael
54k • written 3 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
193
views
Subsetting and merging back Seurat Object brings different results
Seurat
21 hours ago by
Bine
▴ 60
0
votes
1
reply
132
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Winter
• 0
0
votes
1
reply
129
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 1 day ago by
Ram
43k • written 1 day ago by
ernestine.kubi
• 0
1
vote
1
reply
135
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Ruqaiya
• 0
0
votes
1
reply
272
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 3 days ago by
trausch
★ 1.9k • written 20 days ago by
zec018
• 0
1
vote
1
reply
120
views
Super ehancers
enhancers
updated 18 hours ago by
jared.andrews07
★ 16k • written 23 hours ago by
Oburah
• 0
1
vote
1
reply
114
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 18 hours ago by
bk11
★ 2.4k • written 1 day ago by
Jeol
▴ 20
0
votes
0
replies
110
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
3 days ago by
fanglujing
▴ 60
0
votes
0
replies
125
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
3 days ago by
Jacob
• 0
0
votes
0
replies
121
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
122
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
154
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 2 days ago by
Ram
43k • written 2 days ago by
Chakri
• 0
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 2 days ago by
Alexandros
• 0
0
votes
0
replies
25
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
2 hours ago by
Amos Bairoch
▴ 120
0
votes
0
replies
137
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
5 days ago by
tnminh89
▴ 10
0
votes
0
replies
122
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
120
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 3 days ago by
dariober
14k • written 5 days ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
121
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
0
replies
141
views
Filter low express genes in microarray data
microarray
5 days ago by
Chris
▴ 260
0
votes
0
replies
221
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
3 days ago by
SSSJec
• 0
0
votes
0
replies
92
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
0
votes
0
replies
135
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
2 days ago by
O.rka
▴ 710
0
votes
0
replies
565
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
6 days ago by
biocellbio
• 0
0
votes
0
replies
98
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
0
votes
0
replies
88
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 days ago by
Sara
▴ 30
175 results • Page
3 of 4
Recent Votes
Answer: How many reads for WGS Sequencing?
Answer: How many reads for WGS Sequencing?
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
Answer: how to split multi-fasta file into single fasta file named by header
How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
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Recent Replies
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This only works for the first line of sequences.
Answer: What purposes can TPM values be used for?
by
b.contreras.moreira
▴ 180
In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
alifafiq1
• 0
Thank you @AT point. I was planning to use DESeq2 and use the alternate hypothesis (lessAbs) too considering that is the only package that …
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
Comment: HOMER on AWS
by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly
by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
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