Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
2
replies
205
views
PDB related issue
rcsb
pdb
updated 6 days ago by
noodle
▴ 580 • written 6 days ago by
Nafi
• 0
0
votes
0
replies
114
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
6 days ago by
carlopecoraro2
★ 2.5k
0
votes
8
replies
437
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 4 days ago by
LauferVA
4.2k • written 6 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 6 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
487
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
6 days ago by
ashaneev07
▴ 20
1
vote
2
replies
185
views
Downloading full alignments from Pfam
pfam
1 hour ago by
bef1
• 0
0
votes
1
reply
753
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 7 days ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
3
votes
2
replies
299
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 6 days ago by
i.sudbery
19k • written 8 days ago by
vanbelj
▴ 40
0
votes
0
replies
123
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 5 days ago by
dariober
14k • written 7 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
306
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 6 days ago by
ATpoint
82k • written 7 days ago by
Francesco
▴ 10
0
votes
0
replies
140
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
7 days ago by
tnminh89
▴ 10
0
votes
0
replies
146
views
Filter low express genes in microarray data
microarray
7 days ago by
Chris
▴ 260
0
votes
1
reply
337
views
absolute path for symbolic links in Snakefile
Snakemake
updated 7 days ago by
Jesse
▴ 740 • written 15 days ago by
yifangt86
▴ 60
0
votes
2
replies
359
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 7 days ago by
Jesse
▴ 740 • written 10 days ago by
Broccoli
• 0
4
votes
3
replies
370
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 7 days ago by
Arup Ghosh
3.2k • written 8 days ago by
chaco001
▴ 40
1
vote
3
replies
396
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 6 days ago by
Mensur Dlakic
★ 27k • written 8 days ago by
O.rka
▴ 710
0
votes
2
replies
263
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
8 days ago by
Guille
• 0
4
votes
2
replies
305
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
5 days ago by
pairedttest
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 8 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
571
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
8 days ago by
biocellbio
• 0
4
votes
8
replies
671
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 8 days ago by
Alex Reynolds
35k • written 9 days ago by
J
▴ 10
4
votes
7
replies
713
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 8 days ago by
dsull
★ 6.0k • written 12 days ago by
qudrat.nii
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 9 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
3
votes
2
replies
334
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 9 days ago by
dsull
★ 6.0k • written 9 days ago by
Aaliya
▴ 10
3
votes
0
replies
212
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 8 days ago by
Ram
43k • written 9 days ago by
Claire Watson
▴ 60
0
votes
2
replies
295
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 8 days ago by
Ram
43k • written 9 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
206
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
9 days ago by
HarperReed
• 0
3
votes
3
replies
315
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 9 days ago by
GenoMax
142k • written 9 days ago by
sapuizait
▴ 10
1
vote
0
replies
161
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
9 days ago by
KABILAN
▴ 70
0
votes
0
replies
178
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 8 days ago by
Ram
43k • written 9 days ago by
SineWave
• 0
0
votes
0
replies
173
views
RNA-seq: full length gene
RNA-seq
updated 8 days ago by
Ram
43k • written 9 days ago by
Nargis
• 0
1
vote
7
replies
508
views
gvcf joint calling
WES
GATK
VCF
gVCF
7 days ago by
zihanss
• 0
0
votes
0
replies
158
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
9 days ago by
turcoa1
• 0
3
votes
3
replies
332
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 9 days ago by
swbarnes2
14k • written 9 days ago by
M
• 0
0
votes
0
replies
169
views
Designing single-stable RNA molecules
structure
RNA
9 days ago by
Edna
• 0
0
votes
0
replies
180
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
9 days ago by
simplitia
▴ 130
1
vote
1
reply
239
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 9 days ago by
ATpoint
82k • written 9 days ago by
AaronJaime
• 0
0
votes
2
replies
307
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 9 days ago by
GenoMax
142k • written 10 days ago by
Begonia_pavonina
▴ 150
0
votes
3
replies
405
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
5 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
350
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
7 days ago by
Francesco
▴ 10
1
vote
7
replies
525
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 6 days ago by
bk11
★ 2.4k • written 10 days ago by
starswillfade
▴ 10
0
votes
0
replies
169
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 9 days ago by
Ram
43k • written 9 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
165
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
9 days ago by
Emily
▴ 10
1
vote
0
replies
176
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
9 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
161
views
how to read graph_test output of monocle 3
monocle3
9 days ago by
synat.keam
▴ 100
1
vote
0
replies
213
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
9 days ago by
Assaf
▴ 10
0
votes
1
reply
511
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 9 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
3
votes
4
replies
383
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
9 days ago by
QX
• 0
2
votes
1
reply
250
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 10 days ago by
Adrian Altenhoff
★ 1.1k • written 10 days ago by
hemantcnaik
• 0
0
votes
0
replies
159
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
10 days ago by
Aspire
▴ 330
1,000 results • Page
4 of 20
Recent Votes
Answer: LD-prune variants while maintaining a list of SNPs
Comment: TaxID mapping file
Answer: LD-prune variants while maintaining a list of SNPs
Comment: Downloading full alignments from Pfam
Answer: Segmentation error while using a tool
What is the best way to rank genes for GSEA?
What is the best way to rank genes for GSEA?
Recent Locations •
All
Brazil,
just now
United States,
1 minute ago
UCLA,
1 minute ago
Russia,
2 minutes ago
Croatia,
2 minutes ago
United States,
5 minutes ago
Türkiye,
5 minutes ago
Recent Awards •
All
Popular Question
to
iamsmor
• 0
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
Sara
▴ 30
Popular Question
to
Assa Yeroslaviz
★ 1.8k
Popular Question
to
Yoosef
▴ 60
Popular Question
to
Zhenyu Zhang
★ 1.2k
Popular Question
to
psm
▴ 130
Recent Replies
Answer: LD-prune variants while maintaining a list of SNPs
by
Jautis
▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data
by
drajangirija
• 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
by
bef1
• 0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
Comment: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Expe
by
Mensur Dlakic
★ 27k
Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
★ 1.2k
If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
★ 1.2k
These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 30
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Traffic: 1502 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6