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116,666 results • Page
1 of 2334
Sort: Rank
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0
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1
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Differential Accessibility
DiffBind
just now by
Shloka
• 0
0
votes
2
replies
22
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated just now by
GenoMax
141k • written 41 minutes ago by
kim
• 0
0
votes
1
reply
178
views
Extract protein sequence
fasta
alignment
blast
updated 3 hours ago by
Ram
43k • written 2 days ago by
anna
▴ 20
0
votes
0
replies
31
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 3 hours ago by
Ram
43k • written 3 hours ago by
kl
▴ 10
0
votes
3
replies
169
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 4 hours ago by
noodle
▴ 570 • written 15 hours ago by
WUSCHEL
▴ 750
0
votes
4
replies
141
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 hour ago by
Wayne
★ 2.0k • written 7 hours ago by
Mariana
▴ 10
0
votes
1
reply
66
views
metagenomic virome quality assessment
viromics
metagenomics
updated 3 hours ago by
Ram
43k • written 7 hours ago by
Petchimuthu
• 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
3
votes
7
replies
150
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 hours ago by
salias
• 0
0
votes
0
replies
33
views
Using limma in methylation EM-seq?
EM-seq
methylation
4 hours ago by
Lluís R.
★ 1.2k
4
votes
7
replies
470
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
4 hours ago by
e.r.zakiev
▴ 200
0
votes
0
replies
42
views
Synteny analysis
bacterial
synteny
genome
updated 5 hours ago by
GenoMax
141k • written 5 hours ago by
Namil
• 0
0
votes
2
replies
80
views
Genbank File Format
gbkformat
updated 4 hours ago by
Mensur Dlakic
★ 27k • written 5 hours ago by
alenew.am
• 0
0
votes
5
replies
276
views
How should I make kallisto indexes?
kallisto
updated 3 hours ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
63
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
5 hours ago by
SSSJec
• 0
0
votes
3
replies
106
views
Software to separate reads from different individuals
software
development
nanopore
updated 1 hour ago by
GenoMax
141k • written 6 hours ago by
njornet
▴ 20
0
votes
0
replies
37
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
6 hours ago by
David
• 0
3
votes
5
replies
171
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 6 hours ago by
dsull
★ 5.9k • written 9 hours ago by
Kazo
▴ 10
0
votes
2
replies
93
views
How to update R on ubuntu
installation
update
R
apt-get
6 hours ago by
Bosberg
▴ 50
3
votes
0
replies
60
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
8 hours ago by
Biostar
2.7k
0
votes
1
reply
83
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 8 hours ago by
GenoMax
141k • written 13 hours ago by
Ruqaiya
• 0
0
votes
1
reply
235
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 8 hours ago by
trausch
★ 1.9k • written 17 days ago by
zec018
• 0
0
votes
0
replies
54
views
LEfSe
LEfSe
9 hours ago by
benkosta
• 0
0
votes
0
replies
43
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
7 hours ago by
Sara
▴ 30
1
vote
4
replies
316
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
6 hours ago by
hagl
▴ 10
0
votes
1
reply
85
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 10 hours ago by
Mohamed Abderrahmane
▴ 20 • written 10 hours ago by
matteo.levorato
• 0
0
votes
2
replies
95
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
10 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
93
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 12 hours ago by
i.sudbery
19k • written 12 hours ago by
DOBI
• 0
0
votes
0
replies
61
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
13 hours ago by
atharvakarkare14
▴ 10
5
votes
16
replies
553
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
13 hours ago by
Ruqaiya
• 0
0
votes
2
replies
98
views
What should I consider as FASTA for dataset?
PDB
FASTA
14 minutes ago by
Nafi
• 0
34
votes
22
replies
1.5k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
2 hours ago by
noodle
▴ 570
0
votes
0
replies
51
views
Differential accessibility using DiffBinf
diffbind
15 hours ago by
Shloka
• 0
0
votes
0
replies
56
views
vg call vs vg surject
vg
variation
graphs
updated 8 hours ago by
GenoMax
141k • written 15 hours ago by
aliraza3119
• 0
0
votes
1
reply
86
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 8 hours ago by
GenoMax
141k • written 16 hours 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 20 hours ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
165
views
Finding batch and outlayers
Pca
updated 11 hours ago by
christopher medway
▴ 450 • written 20 hours ago by
Tigran
• 0
2
votes
2
replies
153
views
PDB related issue
rcsb
pdb
updated 21 hours ago by
noodle
▴ 570 • written 1 day ago by
Nafi
• 0
0
votes
0
replies
82
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
11 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
299
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 7 hours ago by
dsull
★ 5.9k • written 1 day ago by
jinyu
▴ 10
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 15 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
408
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
1 day ago by
ashaneev07
▴ 20
0
votes
1
reply
130
views
Downloading full alignments from Pfam
pfam
updated 1 day ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
1
reply
721
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 1 day ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
2
votes
2
replies
251
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 11 hours ago by
i.sudbery
19k • written 3 days ago by
vanbelj
▴ 40
0
votes
0
replies
94
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 4 hours ago by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
250
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
119
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
124
views
Filter low express genes in microarray data
microarray
2 days ago by
Chris
▴ 260
0
votes
1
reply
310
views
absolute path for symbolic links in Snakefile
Snakemake
updated 2 days ago by
Jesse
▴ 740 • written 10 days ago by
yifangt86
▴ 60
116,666 results • Page
1 of 2334
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Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
Answer: How to use limma to find differentially expressed genes in response to a continu
Answer: How to use limma to find differentially expressed genes in response to a continu
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Recent Replies
Comment: Landmark gene selection in L1000.
by
GenoMax
141k
Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/
Comment: What should I consider as FASTA for dataset?
by
Nafi
• 0
Protein attribute prediction
Comment: Batch effects : ComBat or removebatcheffects (limma package) ?
by
cwwong13
▴ 40
@kevin May I know whether your comments and edits were mainly based on the fact that "Previously, [crazy] people had been using the origina…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 570
> Can you clarify what you mean by "100% of reads pass cutadapt, even > though 70% of reads contain adapters and get trimmed. The header o…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
by
Matthias Zepper
4.5k
You didn't mention what kind of organism you are working with and what kind of protein you are looking for? If it happens to be a microbia…
Comment: How to use limma to find differentially expressed genes in response to a continu
by
pairedttest
▴ 10
Thank you Gordon for your expertise. One question that I have now that I have a list of DE genes is how to interpret logFC of this continuo…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Yes I plan to use QIIME2, but I'm Cutadapting outside QIIME so its easier to MultiQC without importing/unzipping QZAs (and QIIME2 importing…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
> 3' adapters were removed aprox. 90 times each one, so there sohuld not be read-through at all here Then you have data that has poor Q sc…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Following your advice, I checked the primer and adapters sequences and edited the question accordingly
Comment: How should I make kallisto indexes?
by
dsull
★ 5.9k
We can't phase them out per se, because ``kallisto index`` is still the engine responsible for creating the index under the hood (and there…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
Medhat
9.7k
"./." in your gVCF files typically indicates a lack of information or uncertainty about the genotype at that particular position. This co…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Fungal ITS2 region (length is really variable so read-through can be an issue)
Answer: Is it possible to bulk download files from GEO repository?
by
noodle
▴ 570
Also try the NCBI AWS bucket transfer tool. It's extremely convenient, however it's not instantaneous and you need to have a (paid) AWS acc…
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