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116,676 results • Page
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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
just now by
David Langenberger
11k
0
votes
0
replies
6
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
1 minute ago by
Dora
▴ 10
0
votes
0
replies
1
view
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
just now by
8armed
• 0
0
votes
1
reply
31
views
Deseq2
Deseq2
updated 47 minutes ago by
Jack Tierney
▴ 360 • written 1 hour ago by
Sudip
• 0
0
votes
1
reply
74
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 1 hour ago by
Michael
54k • written 11 hours ago by
Lissa Cruz Saavedra
• 0
1
vote
4
replies
82
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 57 minutes ago by
Lluís R.
★ 1.2k • written 3 hours ago by
이민경[학생](대학원 융합의과학과)
• 0
1
vote
2
replies
41
views
MA plot of shrunken fold change
MA
plot
Deseq2
1 hour ago by
Sudip
• 0
1
vote
1
reply
29
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
count
file
error
in
feature
updated 44 minutes ago by
Michael
54k • written 1 hour ago by
Ravita
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
21
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 hours ago by
Adyasha
• 0
0
votes
0
replies
35
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
5 hours ago by
fanglujing
▴ 60
0
votes
0
replies
52
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
7 hours ago by
Jacob
• 0
0
votes
3
replies
652
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 8 hours ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
148
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 3 hours ago by
Ram
43k • written 10 hours ago by
Hamtaro
▴ 50
0
votes
1
reply
107
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 11 hours ago by
LChart
3.9k • written 16 hours ago by
kl
▴ 10
0
votes
1
reply
93
views
Differential Accessibility
DiffBind
updated 11 hours ago by
Ram
43k • written 12 hours ago by
Shloka
• 0
0
votes
2
replies
135
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
6 hours ago by
kim
• 0
3
votes
2
replies
270
views
Extract protein sequence
fasta
alignment
blast
11 hours ago by
anna
▴ 20
0
votes
3
replies
207
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 16 hours ago by
noodle
▴ 570 • written 1 day ago by
WUSCHEL
▴ 750
0
votes
4
replies
211
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 13 hours ago by
Wayne
★ 2.0k • written 19 hours ago by
Mariana
▴ 10
0
votes
1
reply
89
views
metagenomic virome quality assessment
viromics
metagenomics
updated 16 hours ago by
Ram
43k • written 19 hours ago by
Petchimuthu
• 0
3
votes
7
replies
216
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
15 hours ago by
salias
• 0
0
votes
0
replies
58
views
Using limma in methylation EM-seq?
EM-seq
methylation
17 hours ago by
Lluís R.
★ 1.2k
4
votes
7
replies
501
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
16 hours ago by
e.r.zakiev
▴ 200
0
votes
0
replies
67
views
Synteny analysis
bacterial
synteny
genome
updated 17 hours ago by
GenoMax
141k • written 17 hours ago by
Namil
• 0
0
votes
4
replies
121
views
Genbank File Format
gbkformat
47 minutes ago by
alenew.am
• 0
0
votes
5
replies
319
views
How should I make kallisto indexes?
kallisto
updated 16 hours ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
133
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
18 hours ago by
SSSJec
• 0
0
votes
3
replies
159
views
Software to separate reads from different individuals
software
development
nanopore
updated 14 hours ago by
GenoMax
141k • written 18 hours ago by
njornet
▴ 20
0
votes
0
replies
60
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
18 hours ago by
David
• 0
4
votes
5
replies
212
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 19 hours ago by
dsull
★ 5.9k • written 22 hours ago by
Kazo
▴ 10
0
votes
2
replies
125
views
How to update R on ubuntu
installation
update
R
apt-get
18 hours ago by
Bosberg
▴ 50
4
votes
0
replies
92
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
20 hours ago by
Biostar
2.7k
0
votes
1
reply
104
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
Ruqaiya
• 0
0
votes
1
reply
254
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 21 hours ago by
trausch
★ 1.9k • written 17 days ago by
zec018
• 0
0
votes
0
replies
77
views
LEfSe
LEfSe
21 hours ago by
benkosta
• 0
0
votes
0
replies
65
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
19 hours ago by
Sara
▴ 30
1
vote
4
replies
337
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
19 hours ago by
hagl
▴ 10
0
votes
1
reply
109
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 22 hours ago by
Mohamed Abderrahmane
▴ 20 • written 22 hours ago by
matteo.levorato
• 0
0
votes
2
replies
117
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
22 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
114
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
DOBI
• 0
0
votes
0
replies
81
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
1 day ago by
atharvakarkare14
▴ 10
5
votes
16
replies
582
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
1 day ago by
Ruqaiya
• 0
0
votes
2
replies
163
views
What should I consider as FASTA for dataset?
PDB
FASTA
12 hours ago by
Nafi
• 0
34
votes
23
replies
1.6k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 3 hours ago by
Philipp Bayer
8.4k • written 2 days ago by
noodle
▴ 570
0
votes
0
replies
71
views
Differential accessibility using DiffBinf
diffbind
1 day ago by
Shloka
• 0
0
votes
0
replies
80
views
vg call vs vg surject
vg
variation
graphs
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
aliraza3119
• 0
0
votes
1
reply
108
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
Winter
• 0
2
votes
7
replies
1.2k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 1 day ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
183
views
Finding batch and outlayers
Pca
updated 1 day ago by
christopher medway
▴ 450 • written 1 day ago by
Tigran
• 0
116,676 results • Page
1 of 2334
Recent Votes
Answer: blasting genome contigs against local SILVA 16S RNA database
blasting genome contigs against local SILVA 16S RNA database
Comment: Integrate transcriptomic data and proteomics data.
Comment: MA plot of shrunken fold change
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
Answer: How to find rna strand direction before alignment?
How to work out Z score for heatmaps for RNA seq dataset
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Recent Awards •
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Popular Question
to
kamhamea
• 0
Teacher
to
ATpoint
82k
Popular Question
to
fanglujing
▴ 60
Commentator
to
Philipp Bayer
8.4k
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geneontologyhelp
▴ 390
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elcortegano
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Gordon Smyth
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Recent Replies
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
How would I check if these reads are aligning to regions where there is no expressed sequence know? Should I follow the suggestion of i.sud…
Answer: Deseq2
by
Jack Tierney
▴ 360
[This vignette][1] is a great place to start. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.ht…
Comment: Genbank File Format
by
alenew.am
• 0
Thanks, yes i have tried first here looking for a easier solution (for me), i didnt' know if this format was already available somewhere. t…
Comment: Genbank File Format
by
alenew.am
• 0
Yes, it would be fine with an external solution, thanks for the reply
Answer: Polishing genome assembly
by
Michael
54k
If you have Hifi reads your error rate should already be quite good, therefore polishing with potentially longer and slightly more error-pr…
Comment: Integrate transcriptomic data and proteomics data.
by
Lluís R.
★ 1.2k
You don't need to subset for common features, there are tools that work for that like RGCCA, mixOmics. See for instance a classification [h…
Answer: Integrate transcriptomic data and proteomics data.
by
KABILAN
▴ 50
You can use R package named 'mixOmics' to integrate the datasets. Kindly go through the manual of this package.
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
by
Michael
54k
You will have to describe your problem in much more detail, we are unable to understand what the problem even is. > Please, anyone, sugge…
Comment: MA plot of shrunken fold change
by
Sudip
• 0
Thank you.
Comment: MA plot of shrunken fold change
by
ATpoint
82k
You will need to relevel to make all comparisons available as coefficients, see https://www.biostars.org/p/448959/, or just use ashr shrink…
Comment: Integrate transcriptomic data and proteomics data.
by
Ram
43k
Please define "combine" and "integrate" as best as you can. How do you picture the final product of this task?
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
just k-mer counts (HashingVectorizer + Naive Bayes Classifier). I stayed away from looking at quality scores so far, simulators are usually…
Comment: Landmark gene selection in L1000.
by
kim
• 0
thank you for reply, but i want some information for what microarray data are selected for L1000. thank you!
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
weidonglu
• 0
The reason for your problem was most likely due to you relative complex data and too little system memory. For 20000-30000 transcriptome se…
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴ 80
Your table should look like this (GO terms): ``` geneid GOid Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739 Zm00001eb000020 G…
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