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164 results • Page
2 of 4
Sort: Rank
Rank
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Votes
Replies
0
votes
4
replies
240
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 2 days ago by
Ram
43k • written 2 days ago by
Hamtaro
▴ 50
0
votes
1
reply
170
views
Differential Accessibility
DiffBind
updated 2 days ago by
Ram
43k • written 2 days ago by
Shloka
• 0
0
votes
3
replies
263
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 1 day ago by
GenoMax
141k • written 2 days ago by
kim
• 0
3
votes
2
replies
351
views
Extract protein sequence
fasta
alignment
blast
1 day ago by
anna
▴ 20
3
votes
3
replies
301
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 2 days ago by
noodle
▴ 580 • written 3 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
153
views
metagenomic virome quality assessment
viromics
metagenomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Petchimuthu
• 0
3
votes
7
replies
297
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
2 days ago by
salias
• 0
0
votes
0
replies
113
views
Using limma in methylation EM-seq?
EM-seq
methylation
2 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
559
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
2 days ago by
e.r.zakiev
▴ 200
0
votes
0
replies
117
views
Synteny analysis
bacterial
synteny
genome
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Namil
• 0
0
votes
4
replies
226
views
Genbank File Format
gbkformat
1 day ago by
alenew.am
• 0
0
votes
5
replies
386
views
How should I make kallisto indexes?
kallisto
updated 2 days ago by
dsull
★ 5.9k • written 16 days ago by
bioinfo
▴ 150
0
votes
0
replies
205
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
2 days ago by
SSSJec
• 0
0
votes
3
replies
196
views
Software to separate reads from different individuals
software
development
nanopore
updated 2 days ago by
GenoMax
141k • written 2 days ago by
njornet
▴ 20
0
votes
0
replies
89
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
2 days ago by
David
• 0
4
votes
5
replies
268
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 2 days ago by
dsull
★ 5.9k • written 2 days ago by
Kazo
▴ 10
0
votes
2
replies
172
views
How to update R on ubuntu
installation
update
R
apt-get
2 days ago by
Bosberg
▴ 50
4
votes
0
replies
120
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
2 days ago by
Biostar
2.7k
0
votes
1
reply
126
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Ruqaiya
• 0
0
votes
1
reply
269
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 2 days ago by
trausch
★ 1.9k • written 19 days ago by
zec018
• 0
0
votes
0
replies
97
views
LEfSe
LEfSe
2 days ago by
benkosta
• 0
0
votes
0
replies
80
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
2 days ago by
Sara
▴ 30
1
vote
4
replies
373
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
2 days ago by
hagl
▴ 10
0
votes
2
replies
172
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
1 day ago by
matteo.levorato
• 0
0
votes
2
replies
143
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
2 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
133
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
DOBI
• 0
0
votes
0
replies
95
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
2 days ago by
atharvakarkare14
▴ 20
5
votes
16
replies
655
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
2 days ago by
Ruqaiya
• 0
0
votes
2
replies
187
views
What should I consider as FASTA for dataset?
PDB
FASTA
2 days ago by
Nafi
• 0
38
votes
24
replies
1.8k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 1 day ago by
i.sudbery
19k • written 4 days ago by
noodle
▴ 580
0
votes
0
replies
84
views
Differential accessibility using DiffBinf
diffbind
3 days ago by
Shloka
• 0
0
votes
0
replies
92
views
vg call vs vg surject
vg
variation
graphs
updated 2 days ago by
GenoMax
141k • written 3 days ago by
aliraza3119
• 0
0
votes
1
reply
123
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 2 days ago by
GenoMax
141k • written 3 days ago by
Winter
• 0
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 3 days ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
199
views
Finding batch and outlayers
Pca
updated 2 days ago by
christopher medway
▴ 450 • written 3 days ago by
Tigran
• 0
2
votes
2
replies
191
views
PDB related issue
rcsb
pdb
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
Nafi
• 0
0
votes
0
replies
106
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
405
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 1 day ago by
LauferVA
4.2k • written 3 days 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 3 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
441
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
3 days ago by
ashaneev07
▴ 20
0
votes
1
reply
163
views
Downloading full alignments from Pfam
pfam
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bef1
• 0
0
votes
1
reply
742
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 3 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
284
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 2 days ago by
i.sudbery
19k • written 5 days ago by
vanbelj
▴ 40
0
votes
0
replies
115
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 2 days ago by
dariober
14k • written 3 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
285
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 3 days ago by
ATpoint
82k • written 4 days ago by
Francesco
▴ 10
0
votes
0
replies
134
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
4 days ago by
tnminh89
▴ 10
0
votes
0
replies
138
views
Filter low express genes in microarray data
microarray
4 days ago by
Chris
▴ 260
0
votes
1
reply
321
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Jesse
▴ 740 • written 12 days ago by
yifangt86
▴ 60
0
votes
2
replies
337
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 4 days ago by
Jesse
▴ 740 • written 7 days ago by
Broccoli
• 0
4
votes
3
replies
346
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 4 days ago by
Arup Ghosh
3.2k • written 5 days ago by
chaco001
▴ 40
164 results • Page
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Comment: POSSUM not working due to incompatible pssm file
Comment: Can't install AnnotationHub
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
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Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape?
by
Scooter
▴ 280
Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
Answer: Basic stats in hierfstat
by
mdav
• 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p
by
GenoMax
141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems
by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq
by
Adam
▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject
by
Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
by
Adam
▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
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