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400 results • Page
4 of 8
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
129
views
Synteny analysis
bacterial
synteny
genome
updated 15 days ago by
GenoMax
142k • written 15 days ago by
Namil
• 0
0
votes
4
replies
289
views
Genbank File Format
gbkformat
14 days ago by
alenew.am
• 0
0
votes
0
replies
256
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
15 days ago by
SSSJec
• 0
0
votes
3
replies
241
views
Software to separate reads from different individuals
software
development
nanopore
updated 15 days ago by
GenoMax
142k • written 15 days ago by
njornet
▴ 20
0
votes
2
replies
321
views
How to update R on ubuntu
installation
update
R
apt-get
15 days ago by
Bosberg
▴ 50
0
votes
0
replies
120
views
LEfSe
LEfSe
15 days ago by
benkosta
• 0
0
votes
0
replies
96
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
15 days ago by
Sara
▴ 30
0
votes
2
replies
180
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
15 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
111
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 21 hours ago by
Ram
43k • written 15 days ago by
atharvakarkare14
▴ 30
0
votes
2
replies
225
views
What should I consider as FASTA for dataset?
PDB
FASTA
14 days ago by
Nafi
• 0
0
votes
0
replies
601
views
Differential accessibility using DiffBinf
diffbind
15 days ago by
Shloka
• 0
0
votes
0
replies
105
views
vg call vs vg surject
vg
variation
graphs
updated 15 days ago by
GenoMax
142k • written 15 days ago by
aliraza3119
• 0
0
votes
1
reply
231
views
Finding batch and outlayers
Pca
updated 15 days ago by
christopher medway
▴ 460 • written 15 days ago by
Tigran
• 0
2
votes
2
replies
231
views
PDB related issue
rcsb
pdb
updated 15 days ago by
noodle
▴ 580 • written 15 days ago by
Nafi
• 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 15 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
1
vote
2
replies
267
views
Downloading full alignments from Pfam
pfam
9 days ago by
bef1
• 0
0
votes
0
replies
136
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 15 days ago by
dariober
14k • written 16 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
364
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 16 days ago by
ATpoint
82k • written 16 days ago by
Francesco
▴ 10
0
votes
0
replies
151
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
16 days ago by
tnminh89
▴ 10
0
votes
0
replies
157
views
Filter low express genes in microarray data
microarray
16 days ago by
Chris
▴ 280
0
votes
0
replies
585
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
17 days ago by
biocellbio
• 0
0
votes
0
replies
219
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
18 days ago by
HarperReed
• 0
1
vote
0
replies
170
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
18 days ago by
KABILAN
▴ 70
0
votes
0
replies
189
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 17 days ago by
Ram
43k • written 18 days ago by
SineWave
• 0
0
votes
0
replies
189
views
RNA-seq: full length gene
RNA-seq
updated 18 days ago by
Ram
43k • written 18 days ago by
Nargis
• 0
0
votes
0
replies
169
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
18 days ago by
turcoa1
• 0
0
votes
0
replies
182
views
Designing single-stable RNA molecules
structure
RNA
18 days ago by
Edna
• 0
0
votes
0
replies
192
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
18 days ago by
simplitia
▴ 130
1
vote
1
reply
262
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 18 days ago by
ATpoint
82k • written 18 days ago by
AaronJaime
• 0
0
votes
0
replies
177
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
15 hours ago by
Emily
▴ 20
1
vote
0
replies
190
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
19 days ago by
rohitsatyam102
▴ 860
0
votes
0
replies
173
views
how to read graph_test output of monocle 3
monocle3
19 days ago by
synat.keam
▴ 100
0
votes
1
reply
529
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 19 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
0
votes
0
replies
171
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
19 days ago by
Aspire
▴ 330
0
votes
4
replies
407
views
Highest variable features in single cell data
single-cell
7 days ago by
carolofharvest
▴ 40
1
vote
3
replies
441
views
PCA plot
DESeq2
PCAplot
updated 16 days ago by
LauferVA
4.2k • written 19 days ago by
Aaliya
▴ 10
0
votes
0
replies
167
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
19 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
307
views
Annovar using R package
Annovar
gnomAD
R
18 days ago by
DKA
▴ 40
0
votes
5
replies
434
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 19 days ago by
GenoMax
142k • written 20 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
166
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 20 days ago by
Ram
43k • written 20 days ago by
glaciya2018
• 0
0
votes
0
replies
326
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
20 days ago by
pramach1
▴ 40
0
votes
1
reply
202
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 20 days ago by
Sofia
• 0 • written 20 days ago by
mawigoj318
• 0
0
votes
0
replies
166
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
20 days ago by
salias
• 0
0
votes
5
replies
449
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 17 days ago by
Istvan Albert
100k • written 20 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
140
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 20 days ago by
Ram
43k • written 20 days ago by
newuser2024
• 0
1
vote
2
replies
277
views
alignment result
RNA-seq
samtools
hisat2
19 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
137
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
20 days ago by
Kash
▴ 110
0
votes
1
reply
188
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 20 days ago by
Mensur Dlakic
★ 27k • written 20 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
332
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 20 days ago by
Ram
43k • written 20 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
931
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 20 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
400 results • Page
4 of 8
Recent Votes
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
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Recent Replies
Answer: RNAseq RNA content
by
noodle
▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
by
wyuan37
• 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file?
by
wyuan37
• 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses
by
LauferVA
4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
GenoMax
142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
• 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content
by
ntsopoul
▴ 60
I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: RNAseq RNA content
by
ATpoint
82k
What is "row RNA"?
Comment: Overlapping Ranges within Granges object
by
ATpoint
82k
I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
by
J.
▴ 40
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs?
by
GenoMax
142k
AFAIK "MANE" project is only for human protein-coding genes. One potential explanation. Out of the 2000 ID's only 125 may be MANE. https:…
Answer: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
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