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179 results • Page
3 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
5
replies
404
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
dsull
★ 5.9k • written 18 days ago by
bioinfo
▴ 150
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
3
replies
212
views
Software to separate reads from different individuals
software
development
nanopore
updated 3 days ago by
GenoMax
142k • written 4 days ago by
njornet
▴ 20
0
votes
0
replies
92
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
4 days ago by
David
• 0
0
votes
2
replies
209
views
How to update R on ubuntu
installation
update
R
apt-get
4 days ago by
Bosberg
▴ 50
4
votes
0
replies
130
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
4 days ago by
Biostar
2.7k
1
vote
1
reply
139
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 4 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 4 days ago by
trausch
★ 1.9k • written 20 days ago by
zec018
• 0
0
votes
0
replies
102
views
LEfSe
LEfSe
4 days ago by
benkosta
• 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
4 days ago by
Sara
▴ 30
1
vote
4
replies
388
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
4 days ago by
hagl
▴ 10
0
votes
5
replies
280
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 6 hours ago by
Mohamed Abderrahmane
▴ 20 • written 4 days ago by
matteo.levorato
• 0
0
votes
2
replies
153
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
4 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
143
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
0
replies
97
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
4 days ago by
atharvakarkare14
▴ 30
7
votes
16
replies
705
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
4 days ago by
Ruqaiya
• 0
0
votes
2
replies
197
views
What should I consider as FASTA for dataset?
PDB
FASTA
3 days ago by
Nafi
• 0
38
votes
24
replies
1.9k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 3 days ago by
i.sudbery
19k • written 5 days ago by
noodle
▴ 580
0
votes
0
replies
143
views
Differential accessibility using DiffBinf
diffbind
4 days ago by
Shloka
• 0
0
votes
0
replies
94
views
vg call vs vg surject
vg
variation
graphs
updated 4 days ago by
GenoMax
142k • written 4 days ago by
aliraza3119
• 0
0
votes
1
reply
133
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 4 days ago by
GenoMax
142k • written 4 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 4 days ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
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
2
votes
2
replies
195
views
PDB related issue
rcsb
pdb
updated 4 days ago by
noodle
▴ 580 • written 4 days ago by
Nafi
• 0
0
votes
0
replies
110
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
428
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 2 days ago by
LauferVA
4.2k • written 4 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 4 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
453
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
4 days ago by
ashaneev07
▴ 20
0
votes
1
reply
168
views
Downloading full alignments from Pfam
pfam
updated 4 days ago by
GenoMax
142k • written 5 days ago by
bef1
• 0
0
votes
1
reply
748
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 5 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
292
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 4 days ago by
i.sudbery
19k • written 6 days ago by
vanbelj
▴ 40
0
votes
0
replies
121
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
1
vote
3
replies
298
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Francesco
▴ 10
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
142
views
Filter low express genes in microarray data
microarray
5 days ago by
Chris
▴ 260
0
votes
1
reply
332
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
2
replies
341
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 5 days ago by
Jesse
▴ 740 • written 8 days ago by
Broccoli
• 0
4
votes
3
replies
361
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 5 days ago by
Arup Ghosh
3.2k • written 6 days ago by
chaco001
▴ 40
1
vote
3
replies
384
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 4 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
O.rka
▴ 710
0
votes
2
replies
255
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
6 days ago by
Guille
• 0
4
votes
2
replies
299
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
3 days ago by
pairedttest
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 6 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
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
4
votes
8
replies
648
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 6 days ago by
Alex Reynolds
35k • written 7 days ago by
J
▴ 10
4
votes
7
replies
687
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 6 days ago by
dsull
★ 5.9k • written 10 days ago by
qudrat.nii
▴ 10
3
votes
0
replies
207
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 6 days ago by
Ram
43k • written 7 days ago by
Claire Watson
▴ 60
0
votes
2
replies
281
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 6 days ago by
Ram
43k • written 7 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
176
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 6 days ago by
Ram
43k • written 7 days ago by
SineWave
• 0
0
votes
0
replies
172
views
RNA-seq: full length gene
RNA-seq
updated 6 days ago by
Ram
43k • written 7 days ago by
Nargis
• 0
1
vote
7
replies
492
views
gvcf joint calling
WES
GATK
VCF
gVCF
5 days ago by
zihanss
• 0
179 results • Page
3 of 4
Recent Votes
How to interpret DEXseq results in therms of significance
Answer: High Malat-1 expression in single cell data
Understanding ATAC-seq data
High Malat-1 expression in single cell data
Answer: DSEQ2 analysis
High Malat-1 expression in single cell data
Convert vcf files with phased genotypes to standard haplotype format
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Recent Replies
Answer: IGV interpretation for ATM gene for chromosome 11 for a deceased partient
by
mikemakaveli1
• 0
how can I interpret the mutation for the gene of ATM
Comment: How does gene length effect the number of reads mapped
by
dsull
★ 5.9k
Alicia Oshlack has done some cool work on this but even the plots in her papers show that TPMs sometimes overcorrect and the relationship i…
Comment: Raw counts using stringtie
by
ahmad.sajad4541
• 0
![stringtie error][1] [1]: /media/images/6475a009-e1a6-412b-8515-a8aec173
Answer: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![The below image contains the code and result also.][1] [1]: /media/images/96562b96-d508-4f67-96d1-7c71aa17
Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
My response above was actually partly inspired off of a reading of your paper :)
Comment: Differential Expression Analysis using DESeq2 in R
by
ATpoint
82k
> everything is showing equal in environment section. But when I am checking for equalities, it’s showing False No idea what this means. P…
Answer: Analysis of intronic reads included scRNA-seq data
by
t.montserrat.ayuso
▴ 10
You can calculate the percentage of intronic reads for each cell using the [DropletQC][1] package for R. In this preprint we discuss th…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
I did say almost - obviously things are going to get tricky at gene ends - this is why we have the concept of effective length. Its interst…
Answer: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 10
Malat1 correlates with the intronic content and can be used as a nuclear indicator. In this preprint we discuss about this artifact and the…
Comment: How does gene length effect the number of reads mapped
by
dsull
★ 5.9k
I wouldn't say it's true that number of reads is linearly proportional to the length of the gene. That's just an assumption that people mak…
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
by
dthorbur
★ 1.9k
Using any of the species present would likely result in a resonable annotation set. You could use *Arabidopsis* since it likely has the mos…
Comment: Downloading older version of a tool
by
GenoMax
142k
Have you tried conda install <pkg>=<version> so conda install smalt=0.5.8 <!-- junk -->
Comment: Generating mpileup file using samtools
by
Joe
21k
Older versions of software are usually available via distribution tools or the websites. It may require a lot of digging, but its almost ce…
Comment: RNA-seq data for deep learning classification
by
Yuju
• 0
Thank you very much for sharing your advice. Yes, it definitely makes sense that with the use of deep learning, models would learn normalis…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I didn't use the same tool as in the paper...
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