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990 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
4
votes
1
reply
223
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 1 day ago by
zx8754
11k • written 3 days ago by
Jautis
▴ 560
2
votes
2
replies
308
views
Association study using SNP data
Association
Allele
Parentage
SNP
2 days ago by
drajangirija
• 0
0
votes
0
replies
103
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
113
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
2 days ago by
DGTool
• 0
0
votes
0
replies
121
views
Seurat V5 integration
Seurat
samples
integration
combine
2 days ago by
starswillfade
▴ 10
0
votes
1
reply
174
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 1 day ago by
bk11
★ 2.4k • written 2 days ago by
Yoosef
▴ 60
0
votes
1
reply
456
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 2 days ago by
GenoMax
142k • written 2 days ago by
tulip
• 0
3
votes
4
replies
400
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 22 hours ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
SHN
▴ 40
4
votes
2
replies
250
views
GRCh38.gmap file
gnomix
gmap
2 days ago by
lorena9132
▴ 10
2
votes
3
replies
813
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 3 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
1
reply
252
views
creating batch colum for batch correction
batch-correction
combat
1 day ago by
Expert
▴ 10
1
vote
4
replies
343
views
Segmentation error while using a tool
smalt
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
Ruqaiya
• 0
0
votes
1
reply
205
views
Help with DGEList function
DGEList
R
updated 1 day ago by
marco.barr
▴ 90 • written 3 days ago by
Natali
• 0
0
votes
0
replies
148
views
Homer motif analysis
Homer
3 days ago by
daffodil
▴ 10
0
votes
4
replies
289
views
HCL database download
database
HCL
human
updated 8 hours ago by
GenoMax
142k • written 3 days ago by
sooni
▴ 20
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
2 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
291
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 3 days ago by
chrchang523
10k • written 7 days ago by
8armed
▴ 10
0
votes
5
replies
338
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 3 days ago by
chrchang523
10k • written 4 days ago by
curious
▴ 750
0
votes
1
reply
203
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 3 days ago by
Ram
43k • written 4 days ago by
Rob
▴ 170
0
votes
1
reply
195
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Ximena
• 0
0
votes
1
reply
188
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 3 days ago by
Ram
43k • written 4 days ago by
Valentina
• 0
0
votes
6
replies
410
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 3 days ago by
swbarnes2
14k • written 4 days ago by
Erina
• 0
0
votes
2
replies
224
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
1 day ago by
kalavattam
▴ 190
1
vote
3
replies
273
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
2 days ago by
Lada
▴ 30
1
vote
0
replies
144
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 1 day ago by
zx8754
11k • written 4 days ago by
Emilie
▴ 10
0
votes
0
replies
136
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
4 days ago by
Javier
• 0
0
votes
1
reply
229
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 3 days ago by
Thanujay S
• 0 • written 4 days ago by
yahn
• 0
0
votes
0
replies
129
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
4 days ago by
mikemakaveli1
• 0
2
votes
2
replies
213
views
Raw counts using stringtie
stringtie
RNA-seq
updated 4 days ago by
GenoMax
142k • written 4 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
129
views
Modify plot R mtDNA indel
plot
mtDNA
R
4 days ago by
marco.barr
▴ 90
0
votes
0
replies
294
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
4 days ago by
NorbertK
• 0
3
votes
2
replies
228
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 3 days ago by
Ram
43k • written 4 days ago by
carolofharvest
▴ 30
12
votes
13
replies
709
views
High Malat-1 expression in single cell data
single-cell
updated 6 hours ago by
dsull
★ 6.0k • written 8 days ago by
carolofharvest
▴ 30
0
votes
2
replies
245
views
Downloading older version of a tool
Alignment
tools
3 days ago by
Ruqaiya
• 0
0
votes
0
replies
145
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
4 days ago by
rustykb
▴ 20
1
vote
1
reply
185
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 3 days ago by
Ram
43k • written 4 days ago by
adi.gershon1
• 0
3
votes
5
replies
277
views
Generating mpileup file using samtools
mpileup
samtools
updated 4 days ago by
Joe
21k • written 4 days ago by
Ruqaiya
• 0
0
votes
5
replies
356
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 4 days ago by
b.contreras.moreira
▴ 180 • written 5 days ago by
JH
• 0
1
vote
3
replies
284
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Qi
• 0
0
votes
0
replies
136
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
4 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
280
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 4 days ago by
dthorbur
★ 1.9k • written 4 days ago by
Vijith
▴ 30
0
votes
0
replies
145
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
4 days ago by
Jeyong
• 0
0
votes
2
replies
730
views
homer not configured properly
Homer
makeTagDirectory
updated 4 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
262
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 4 days ago by
Alex Reynolds
35k • written 5 days ago by
SJP
• 0
0
votes
0
replies
133
views
Empty table plot using plotGseaTable()
FGSEA
3 days ago by
Chris
▴ 280
0
votes
1
reply
182
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 5 days ago by
anovak
▴ 120 • written 5 days ago by
Hang
• 0
1
vote
3
replies
236
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 5 days ago by
jared.andrews07
★ 16k • written 5 days ago by
yvonneh
▴ 10
3
votes
5
replies
319
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
4 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 5 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
196
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
5 days ago by
dtnondorf
• 0
990 results • Page
2 of 20
Recent Votes
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Answer: Understanding STAR output (Aligned.out.sam file)
Comment: High Malat-1 expression in single cell data
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Recent Replies
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v
by
sainavyav22
• 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases
by
jared.andrews07
★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
GenoMax
142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
Comment: Repeated testing/data mining in RNA Seq
by
robert.flynn.21
• 0
Thanks! I'll give it a go.
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
Yes, they are very clear about this. The page about the Vignettes says: >"They are not meant as a comprehensive documentation of all the fe…
Comment: Gene density plot
by
dthorbur
★ 1.9k
This sounds like it would be a simple task in either python or R. Read data in, potentially with a library like `data.table` in `R`, depend…
Answer: HLA-HD tool for genomic imputation
by
Javier
• 0
Hi, I just solved the same error. In my case, it was because I misunderstood the instructions. hlahd.sh -t 4 *-f ~/hlahd.1.7.0/fr…
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