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926 results • Page
3 of 19
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
163
views
Where to get the following bed file?
WES
bed
reference
file
updated 3 days ago by
GenoMax
142k • written 3 days ago by
wyuan37
• 0
0
votes
0
replies
108
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
3 days ago by
Scott McKay
▴ 30
0
votes
0
replies
104
views
Cellphonedb results
cpdb
visulization
cellphonedb
3 days ago by
piotto
▴ 20
0
votes
0
replies
126
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
3 days ago by
belloy
• 0
0
votes
3
replies
235
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 3 days ago by
swbarnes2
14k • written 3 days ago by
Ngrin
• 0
1
vote
6
replies
689
views
anRichment is missing
WGCNA
anRichment
updated 3 days ago by
GenoMax
142k • written 5 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
203
views
Gene ontology and homologs
gene-ontology
updated 3 days ago by
geneontologyhelp
▴ 400 • written 4 days ago by
beshka194
• 0
1
vote
2
replies
223
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 3 days ago by
zx8754
11k • written 4 days ago by
snajafy
• 0
0
votes
0
replies
110
views
Cox Model with interaction item interpretation
Cox
4 days ago by
Bine
▴ 60
0
votes
0
replies
99
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
1 day ago by
Javier
• 0
1
vote
7
replies
478
views
Question regarding WGCNA
WGCNA
Network-construction
1 day ago by
deepak
• 0
0
votes
0
replies
104
views
vdjtools
vdjtools
4 days ago by
yueli7
▴ 250
1
vote
0
replies
142
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
4 days ago by
Biostar
2.7k
0
votes
1
reply
282
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 3 days ago by
andres.firrincieli
3.6k • written 4 days ago by
Antonio
• 0
0
votes
0
replies
115
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 4 days ago by
Ram
43k • written 4 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
100
views
Normalizing AMR gene count data
abundance
RGI
updated 4 days ago by
Ram
43k • written 4 days ago by
arshad1292
▴ 100
1
vote
0
replies
124
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
sarumonsus
▴ 10
1
vote
2
replies
305
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
3 days ago by
M.
▴ 30
0
votes
0
replies
118
views
How to implement an IGV to streamlit app?
python
streamlit
igv
4 days ago by
avigail.shnaider
• 0
1
vote
5
replies
312
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 4 days ago by
Ram
43k • written 4 days ago by
snajafy
• 0
0
votes
2
replies
268
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 4 days ago by
GenoMax
142k • written 4 days ago by
mropri
▴ 150
0
votes
1
reply
301
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 4 days ago by
aaron.stevens
• 0 • written 3 months ago by
sativus
▴ 20
2
votes
2
replies
237
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
4 days ago by
brandon
• 0
0
votes
0
replies
128
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
4 days ago by
KHURRAM SHAHZAD
• 0
1
vote
5
replies
381
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 4 days ago by
Ram
43k • written 5 days ago by
snajafy
• 0
0
votes
0
replies
117
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
4 days ago by
Christopher
• 0
4
votes
1
reply
240
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 4 days ago by
zx8754
11k • written 5 days ago by
Jautis
▴ 560
2
votes
2
replies
323
views
Association study using SNP data
Association
Allele
Parentage
SNP
5 days ago by
drajangirija
• 0
0
votes
0
replies
111
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
121
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
5 days ago by
DGTool
• 0
1
vote
3
replies
296
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 19 hours ago by
bk11
★ 2.4k • written 5 days ago by
Yoosef
▴ 60
0
votes
1
reply
546
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 5 days ago by
GenoMax
142k • written 5 days ago by
tulip
• 0
3
votes
4
replies
423
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 3 days ago by
Gordon Smyth
★ 7.1k • written 6 days ago by
SHN
▴ 40
4
votes
2
replies
260
views
GRCh38.gmap file
gnomix
gmap
5 days ago by
lorena9132
▴ 10
2
votes
3
replies
822
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 5 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
1
reply
261
views
creating batch colum for batch correction
batch-correction
combat
4 days ago by
Expert
▴ 10
1
vote
4
replies
363
views
Segmentation error while using a tool
smalt
updated 6 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
Ruqaiya
• 0
0
votes
1
reply
225
views
Help with DGEList function
DGEList
R
updated 4 days ago by
marco.barr
▴ 100 • written 6 days ago by
Natali
• 0
0
votes
0
replies
156
views
Homer motif analysis
Homer
6 days ago by
daffodil
▴ 10
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
5 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
307
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 6 days ago by
chrchang523
10k • written 10 days ago by
8armed
▴ 10
0
votes
5
replies
354
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 6 days ago by
chrchang523
10k • written 6 days ago by
curious
▴ 750
0
votes
1
reply
215
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 5 days ago by
Ram
43k • written 6 days ago by
Rob
▴ 170
0
votes
1
reply
206
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Ximena
• 0
0
votes
1
reply
202
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 6 days ago by
Ram
43k • written 6 days ago by
Valentina
• 0
0
votes
6
replies
432
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
Erina
• 0
0
votes
2
replies
237
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
3 days ago by
kalavattam
▴ 190
1
vote
3
replies
292
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
4 days ago by
Lada
▴ 30
1
vote
0
replies
151
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 4 days ago by
zx8754
11k • written 6 days ago by
Emilie
▴ 10
0
votes
0
replies
140
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
6 days ago by
Javier
• 0
926 results • Page
3 of 19
Recent Votes
Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
Truncated metadata file report from ENA Portal API
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dthorbur
★ 1.9k
Popular Question
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maria.soler
• 0
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melissachua90
▴ 70
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Recent Replies
Comment: cellranger error message
by
Max
• 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Giulio Genovese
▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
by
Pierre Lindenbaum
161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols
by
Ruqaiya
• 0
What does the star mean then ?
Comment: RNA seq analysis
by
prifa
▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location
by
dthorbur
★ 1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
Comment: Alignment of samples with spike-in
by
GenoMax
142k
> but then if you only allow to map uniquely mapped reads, you are losing spike-in information, How so? Spike-in's are generally unique s…
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