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Limit : this year
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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
4
replies
311
views
Refseq annotation | Populus trichocarpa
R
RNA-seq
plants
Refseq
updated 5 days ago by
Ram
40k • written 6 days ago by
P
• 0
1
vote
1
reply
191
views
Read Counts from BAM file
bam
samtools
qualimap
readcount
updated 6 days ago by
ATpoint
76k • written 6 days ago by
Smriti
• 0
0
votes
2
replies
232
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
5 days ago by
JLee
• 0
0
votes
1
reply
189
views
Identify parent of each read in a GAF
gaf
vgteam
vg
updated 6 days ago by
Jordan M Eizenga
▴ 360 • written 6 days ago by
cfourps
▴ 10
0
votes
3
replies
252
views
Errors while trying to run Scenic
Scenic
updated 6 days ago by
GenoMax
134k • written 6 days ago by
Stavroula
• 0
0
votes
3
replies
265
views
How to find target genes From RNA seq data?
Cotton
DGE
RNA-seq
updated 6 days ago by
Ram
40k • written 6 days ago by
Fizzah
▴ 30
0
votes
0
replies
135
views
maftools - median survival time doesn't match plot
R
survival
maftools
K-M
7 days ago by
BioGuy
• 0
0
votes
1
reply
166
views
vg rna pantranscriptome
rna
vg
updated 6 days ago by
Jordan M Eizenga
▴ 360 • written 7 days ago by
z
• 0
0
votes
0
replies
124
views
Genetic distance in cM from VCF of non-reference species to run Beagle
plink
beagle
vcf
updated 6 days ago by
Ram
40k • written 7 days ago by
AndrMod
• 0
1
vote
4
replies
290
views
rRNA filtering from human RNA-seq data
rRNA
RNA-seq
6 days ago by
deniz
▴ 10
0
votes
5
replies
355
views
manhattan plot with vcf information
R
manhattan
vcf
updated 4 days ago by
dthorbur
▴ 550 • written 7 days ago by
sooni
▴ 10
0
votes
0
replies
547
views
after gatk VariantAnnotator -V *_com_norm.vcf -A AlleleFraction -O *_norm_AB.vcf There "nan,nan" or "nan" in my vcf file
gatk
AlleleFraction
VariantAnnotator
updated 6 days ago by
Ram
40k • written 7 days ago by
zhuo
• 0
2
votes
0
replies
140
views
the dispersion estimation of edgeR and DESeq2
estimation
dipersion
edgeR
DESeq2
7 days ago by
tommy
▴ 30
2
votes
3
replies
287
views
Genewise output help
genewise
updated 7 days ago by
Jean-Karim Heriche
26k • written 7 days ago by
lorenzoedg
• 0
2
votes
1
reply
175
views
Best Tools and Practices for CNV Variant Calling in WES Data
CNV
WES
updated 7 days ago by
Pierre Lindenbaum
157k • written 7 days ago by
Nadav
▴ 10
0
votes
2
replies
193
views
Identify genes for mapped reads with combined human-7HPV genome index
star
samtools
updated 7 days ago by
Ram
40k • written 7 days ago by
r.j.lock
• 0
0
votes
0
replies
124
views
Data for pathview() (KEGG Pathway Map) after EdgeR
EdgeR
LogFC
pathview
KEGG
7 days ago by
Ann
▴ 10
0
votes
0
replies
272
views
GTF/Reference genome adjustments? Gene-based differential expression analysis of genetically modified mouse line
RNA-seq
DGE
updated 7 days ago by
Ram
40k • written 8 days ago by
alex
• 0
0
votes
0
replies
146
views
Selecting SNPs for two-sample Mendelian randomization study/analysis
Two-sample
SNPs
Mendelian
randomization
8 days ago by
huynguyenacademia
• 0
0
votes
0
replies
139
views
cosine simialrity of mutation signature analysis
similarity
Mutational
analysis
signature
cosine
8 days ago by
probioquestioner
• 0
0
votes
1
reply
216
views
Significance testing of top vs. random SNPs
SNPs
significance
variance
statistical
updated 4 days ago by
dthorbur
▴ 550 • written 8 days ago by
am29
▴ 30
3
votes
2
replies
422
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 5 days ago by
yhdist
▴ 70 • written 8 days ago by
Cookin
• 0
0
votes
0
replies
150
views
Why we are using filtering >0 for up and <0 for down after TopTags() to extract de genes ids?
EdgeR
logfc
DEG
8 days ago by
Ann
▴ 10
0
votes
1
reply
174
views
PyMOL: how to list all selection names?
pymol
updated 7 days ago by
Wayne
★ 1.8k • written 8 days ago by
Ondina
▴ 90
2
votes
2
replies
215
views
Clustering algorithm based on grouping sequences into gene families
gene-families
clustering
updated 7 days ago by
Ram
40k • written 8 days ago by
francesco
• 0
0
votes
0
replies
141
views
Homozygous reference genotype for a GIAB genome
GIAB
IDs
reference
rs
Homozygous
8 days ago by
New2R
▴ 60
0
votes
0
replies
146
views
PRSice - Phenotype File Not Read Correctly
PRSice2
9 days ago by
V
• 0
0
votes
2
replies
1.5k
views
Question about REDItools
REDItools
updated 9 days ago by
Ethan Lee
• 0 • written 4.1 years ago by
tujuchuanli
▴ 100
1
vote
5
replies
500
views
Idat raw data conversion
idat
updated 8 days ago by
Giulio Genovese
▴ 330 • written 10 days ago by
Zi
• 0
1
vote
3
replies
351
views
What is "intersectional genetic strategy"? How does it work? What can it do?
cell-subtypes
9 days ago by
Ethan Lee
• 0
0
votes
0
replies
180
views
What metrics to use to calculate variant library evenness or uniformity or bias
library-bias
variant
updated 9 days ago by
Ram
40k • written 10 days ago by
eli_bayat
▴ 90
0
votes
0
replies
200
views
Tools to turn perfect phylogenetic matrix into a tree
parsimony
Phylogeny
tree
10 days ago by
Ritu_K
▴ 10
2
votes
4
replies
434
views
Help with celltype annotation
seurat
single-cell
9 days ago by
Chris
▴ 180
0
votes
1
reply
1.0k
views
Downstream analysis on multi-sample or single-sample VCF files?
next-gen
VCF
updated 10 days ago by
Ram
40k • written 2.8 years ago by
NGSCanBioinf
▴ 10
0
votes
1
reply
655
views
How to get enrichment of ERVs in differentially expressed peaks from ATAC-seq data?
ChIP-Seq
ERVs
ATAC-seq
updated 10 days ago by
pb11
▴ 10 • written 2.8 years ago by
fdemiguelsdp
• 0
3
votes
4
replies
357
views
Weighted analysis
RNA-seq
7 days ago by
Peter
• 0
1
vote
2
replies
270
views
Multiple testing adjustment for stepwise model selection
statistics
8 days ago by
mel22
▴ 100
0
votes
2
replies
291
views
Deseq2 colData for single condition
RNA-seq
10 days ago by
Petesview
• 0
0
votes
0
replies
174
views
PopGenome: there are missing regions when calculating Tajima's D per gene
PopGenome
8 days ago by
Bing
• 0
1
vote
2
replies
283
views
functional analysis prediction
functionalanalysis
metabarcoding
16S
8 days ago by
safeassli
• 0
0
votes
1
reply
224
views
Asymmetric/biased log2FC values for low-expressed genes in DESeq2
DESeq2
DEG
fold-change
updated 10 days ago by
Ram
40k • written 11 days ago by
chenzy
• 0
0
votes
8
replies
959
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
3 days ago by
pb11
▴ 10
0
votes
5
replies
458
views
Convert gene id's to gene symbol preserving gene id's in deseq2
ensembl
r
DE
deseq2
updated 9 days ago by
Ram
40k • written 11 days ago by
dylannicoembros
• 0
1
vote
1
reply
246
views
Bioconductor Package Installation
bioconductor
updated 11 days ago by
Ram
40k • written 11 days ago by
oduduabasi.isaiah
• 0
0
votes
0
replies
201
views
External validation in bioinformatics analyses
External
validation
11 days ago by
Saeedeh Salehi
▴ 10
2
votes
4
replies
373
views
join the control replicates
RNA-seq
updated 11 days ago by
seidel
11k • written 11 days ago by
Jean Pierre
• 0
4
votes
5
replies
487
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
8 days ago by
psm
▴ 100
0
votes
3
replies
311
views
RdRp scan - identifying/detecting viruses- metagenomic workflow- need help
RdRp
virus-detection
metagenomic
updated 7 days ago by
Ram
40k • written 11 days ago by
eric--carron
• 0
1
vote
1
reply
225
views
Is it possible to find the target bed file for TSO500 panel?
bed
illumina
target
updated 11 days ago by
GenoMax
134k • written 11 days ago by
Danchurova
• 0
0
votes
2
replies
263
views
circRNA isolation
circular-RNA
circRNA
cDNA
11 days ago by
dbagmerve
• 0
1,000 results • Page
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Recent Votes
Comment: Quantification after transcriptome assembly with Trinity
Snakemake: output folder a as dependency to a different rule
A: Snakemake: output folder a as dependency to a different rule
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
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Recent Replies
Comment: Calculation of TMB on gene level
by
smrutimayipanda
▴ 20
can you please tell me why it is technically incorrect?
Answer: Gene enrichment analysis of prokaryotes gene
by
dthorbur
▴ 550
[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses. [H…
Comment: Read block operation failed with BAM file
by
John Marshall
3.0k
Indeed, though it is a seek issue when accessing files **over HTTP and other network protocols**. So, unless there's something you didn't m…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
Comment: gene correlations in between two groups
by
ATpoint
76k
And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details. …
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype
by
dthorbur
▴ 550
Hello again. Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Hello Dariober, That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R
by
Nicolas Rosewick
10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
by
Alex Reynolds
35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
by
Alex Reynolds
35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
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