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369 results • Page
3 of 8
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Views
Votes
Replies
0
votes
4
replies
219
views
vector memory exhausted (limit reached?)
escape
seurat
scGSEA
Rstudio.
4 days ago by
50cf32b2
• 0
1
vote
4
replies
398
views
filter out T cell clones
vdjtools
TCR
mixcr
bulk
updated 4 days ago by
Jesse
▴ 450 • written 10 weeks ago by
chi.delta
▴ 40
2
votes
4
replies
185
views
Calculate sequencing file size?
storage
data
sequencing
plan
management
updated 4 days ago by
GenoMax
125k • written 4 days ago by
Lluís R.
★ 1.2k
2
votes
4
replies
251
views
Ensembl ID to Gene Symbol Converter
ensembl
Homo_sapiens
BioMart
biotools
updated 3 days ago by
GenoMax
125k • written 6 days ago by
GA
• 0
2
votes
4
replies
212
views
drop duplicate insertion deletions in VCF at same position while keeping one
bcftools
11 hours ago by
curious
▴ 720
0
votes
4
replies
93
views
Getting a VCF file from plink .bed, .fam and .bim files
vcf
plink
3 hours ago by
hi.there
• 0
0
votes
4
replies
824
views
Detection T cell receptor transcripts
RNA-Seq
sequence
next-gen
updated 5 days ago by
mizraelson
▴ 40 • written 2.5 years ago by
jsw940
▴ 10
6
votes
4
replies
2.9k
views
Generate GVF file from VCF file
VCF
updated 6 days ago by
Alireza
▴ 20 • written 8.1 years ago by
win
▴ 940
2
votes
4
replies
263
views
GSEA on nonmodel organisms
GSEA
RNAseq
transcriptomics
multispecies
R
15 hours ago by
Lada
▴ 10
0
votes
4
replies
248
views
Running command in docker container results in directly shutting down the docker container
docker-container
python
ubuntu
docker
3 days ago by
stan.aanhane
▴ 30
3
votes
4
replies
2.0k
views
Nextseq and Miseq data output difference?
sequencing
updated 5 days ago by
mizraelson
▴ 40 • written 3.9 years ago by
Payal
▴ 140
3
votes
4
replies
262
views
difference between target sequencing technologies
capture
sequencing
hybrid
wes
18 hours ago by
pingu77
▴ 10
0
votes
4
replies
289
views
get SNPs from draft genomes
genome
SNP
updated 4 days ago by
colindaven
4.4k • written 7 days ago by
anubhav9
• 0
2
votes
4
replies
344
views
How to continue a interrupted MrBayes tree analysis?
MrBayes
updated 1 day ago by
omaridris5315
▴ 10 • written 7 days ago by
超
• 0
5
votes
4
replies
585
views
Help and idea with TCR/BCR analysis
BCR
TCR
scRNA-seq
updated 5 days ago by
mizraelson
▴ 40 • written 3 months ago by
fi1d18
★ 4.1k
0
votes
4
replies
690
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
normalization
batcheffect
single_cell_features
training_test_split
updated 1 day ago by
madbadradscientist
▴ 20 • written 5 months ago by
mmitra
▴ 40
0
votes
4
replies
2.6k
views
biomaRt: Extracting data for a particular isoform (R/bioconductor)
bioconductor
utr
biomart
updated 6 days ago by
Ram
37k • written 7.7 years ago by
bsmith030465
▴ 210
3
votes
4
replies
1.9k
views
Distant metastases-free survival Time and Events/Censored data
Prognosis
Cox-Regression
Survival-Analysis
updated 4 hours ago by
Ram
37k • written 7.7 years ago by
Masood
▴ 20
1
vote
4
replies
1.4k
views
Shannon vs Simpson for TCR diversity estimation
TCR
shannon
simpson
updated 4 days ago by
mizraelson
▴ 40 • written 3.8 years ago by
CY
▴ 710
4
votes
3
replies
5.5k
views
Convert Official Gene Symbols To Uniprot Ids In Python ?
convert
gene
uniprot
python
database
updated 13 hours ago by
Francesco
• 0 • written 8.9 years ago by
hicsuntdrac0nis
▴ 240
1
vote
3
replies
242
views
"Error parsing strand (?) from GFF line" happenning in gffread, stringtie and cufflinks
bioinformatics
gffread
gff
stringtie
cufflinks
updated 3 days ago by
Pierre Lindenbaum
152k • written 4 days ago by
Guilherme
• 0
2
votes
3
replies
124
views
mirbase does not have miRNA annotation of my species, what are the alternatives?
mirbase
mirna-seq
2 hours ago by
demoraesdiogo2017
▴ 80
9
votes
3
replies
9.3k
views
How to correctly use the color option in R image() function?
R
image
updated 6 hours ago by
Ram
37k • written 7.7 years ago by
Xianjun
▴ 300
0
votes
3
replies
2.4k
views
Script to assess the transcriptome assembly quality in terms of blastx and tblasn results?
Assembly
blast
RNA-Seq
sequencing
updated 6 days ago by
Ram
37k • written 7.7 years ago by
seta
★ 1.7k
1
vote
3
replies
1.9k
views
how to count un-mapped reads at specific position using samtools?
sequencing
genome
sequence
updated 6 days ago by
Ram
37k • written 7.7 years ago by
mangfu100
▴ 780
3
votes
3
replies
941
views
6 follow
Do companies accept students for Master's Thesis in Germany?
Masters
Industry
Internship
Thesis
updated 6 days ago by
Matthias Zepper
2.8k • written 15 months ago by
Shreyashi
• 0
4
votes
3
replies
217
views
Gviz python alternative
Gviz
Bioconductor
Biopython
python
R
7 hours ago by
bhumm
▴ 10
0
votes
3
replies
208
views
Help converting .CYCHP to .txt or .csv or .vcf
cychp
updated 3 days ago by
Pierre Lindenbaum
152k • written 3 days ago by
Sarah
• 0
0
votes
3
replies
5.0k
views
QQ plot - how to add gris shadow showing confidence interval
qqplot
R
updated 6 hours ago by
Ram
37k • written 7.7 years ago by
aleix.arnau1990
▴ 10
0
votes
3
replies
583
views
CDSeq for deconvolution of whole blood RNAseq, any experience?
RNAseq
Deconvolution
updated 5 days ago by
FrankStarling
▴ 20 • written 15 months ago by
Barista
▴ 20
0
votes
3
replies
324
views
How to compare a Nanopore read (.fastq) to a genome assembly file (.fna)
fastq
genome
dna
Nanopore
updated 3 days ago by
colindaven
4.4k • written 13 days ago by
BananaDNA
• 0
2
votes
3
replies
281
views
What should be control group for differential expression in single cell? either distant normal samples or primary tumors when analysing metastatic sa…
single-cell
transcriptomics
differential-expression
RNAseq
updated 6 days ago by
ATpoint
68k • written 6 days ago by
gorizwango
▴ 30
0
votes
3
replies
2.2k
views
display single dbSNP entry in UCSC genome browser
genome
SNP
dbsnp
updated 6 days ago by
Ram
37k • written 7.7 years ago by
chrisothal
• 0
2
votes
3
replies
716
views
Merging FASTQs from the same sample
Merging
FASTQ
cellranger
scRNAseq
10X
updated 23 hours ago by
Angelina_G
• 0 • written 13 months ago by
adellegreene
• 0
2
votes
3
replies
283
views
SALMON Index build Process Killed!
salmon
index
mapping
5 days ago by
Soumajit
▴ 30
2
votes
3
replies
479
views
setting up Kallisto software
rnaseqanalysis
anaconda
kalliosto
miniconda
software
updated 4 days ago by
ATpoint
68k • written 6 months ago by
bioinformatics
▴ 10
0
votes
3
replies
87
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicFeatures
ORFik
GenomicRanges
updated 4 hours ago by
Ram
37k • written 6 hours ago by
Estefania
▴ 10
2
votes
3
replies
13k
views
Bootstrap values on a phylogenetic tree (RAxML).
PAxML
bootstrap
phylogenetic-tree
updated 6 hours ago by
Ram
37k • written 7.7 years ago by
vasilislenis
▴ 150
0
votes
3
replies
1.8k
views
consistency in sequence alignment?
alignment
sequence
updated 6 days ago by
Ram
37k • written 7.7 years ago by
lait
▴ 170
9
votes
3
replies
397
views
Hugely different results between edgeR and DESeq2
edgeR
RNASeq
Expression
Differential
DESeq2
updated 2 days ago by
Gordon Smyth
★ 5.4k • written 5 days ago by
Gama313
▴ 110
1
vote
3
replies
1.5k
views
Exon Coordinates Of Hg19 Genome related question.. for ExomDepth(CNV analysis)
next-gen
updated 6 days ago by
Joakim
▴ 40 • written 8.6 years ago by
younhee.ko
• 0
1
vote
3
replies
284
views
Alphafold in Linux - HHblits error
linux
alphafold
5 days ago by
charlieclark1ee
▴ 10
0
votes
3
replies
186
views
Reomve the first occurance of overalapping variants from VCF file
vcf
vcftools
updated 6 days ago by
mohammadhassanj
▴ 230 • written 6 days ago by
Frieda
▴ 60
1
vote
3
replies
260
views
How can I construct the adjacency matrix for gene ontology between genes
GeneOntology
python
GO
updated 4 days ago by
barslmn
★ 1.2k • written 4 days ago by
songyeon0425
• 0
0
votes
3
replies
101
views
Downloading 450k methylation data from GEO
minfi
450K
IDAT
Methylation
GEO
updated 5 hours ago by
GenoMax
125k • written 9 hours ago by
Edward E-B
• 0
0
votes
3
replies
1.3k
views
Help with NGS
next-gen
alignment
updated 6 days ago by
Ram
37k • written 7.7 years ago by
Letícia Raposo
• 0
0
votes
3
replies
235
views
fastq-dump unable to separate fastq files from scRNA-seq SRA files
SRA
sratoolkit
fastq-dump
scRNA-seq
6 days ago by
ravihansa82
▴ 110
29
votes
3
replies
14k
views
In Cigar String, What Is The Difference Between 'N' And 'D' ?
cigar
bam
sam
updated 6 days ago by
Ram
37k • written 8.9 years ago by
Chen Sun
★ 1.1k
0
votes
3
replies
106
views
Help interpreting FastQC report
fastQC
trimming
quality-control
updated 6 hours ago by
GenoMax
125k • written 11 hours ago by
sithlordashley
• 0
3
votes
3
replies
316
views
How to select data from assays list in SummarizedExperiment to plot
r
bioconductor
DEP
SummarizedExperiment
3 days ago by
WUSCHEL
▴ 660
369 results • Page
3 of 8
Recent Votes
Answer: Looking for a tool which provides mapping quality score distributions from BAM f
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: Gviz python alternative
Answer: Gviz python alternative
Answer: Annotating snps with gene information
Comment: Plotting Correlation matrix
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Answer: Python Dictionary of Primer3-py Primer Designs
by
barslmn
★ 1.2k
You're so close. You can simply loop over sequence dictionaries like you did with the `design_output` and check if the keys with `startswit…
Comment: Unable to install clusterProfiler on Mac M1
by
GenoMax
125k
Have you installed `Xcode` and the command line tools that go with? If not you will need to install those.
Answer: SRA taxonomy analysis
by
Steve
• 0
Thanks @genomax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/ I wonder if it …
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
by
demoraesdiogo2017
▴ 80
thanks! however, shouldn't it also have a gtf/gff file with the annotations?
Comment: Getting a VCF file from plink .bed, .fam and .bim files
by
hi.there
• 0
Thanks Ram. Yes. I have read all of this documentation before. --file and --bfile. I have actually tried doing the complete liftover be…
Answer: SRA taxonomy analysis
by
GenoMax
125k
This data may only be available using `BigQuery` for [**SRA in cloud**][1]. For more information on querying: https://www.ncbi.nlm.nih.g…
Comment: MesKit error message - Join columns must be present in data.
by
CH1374
• 0
column names for the maf are: [1] "Hugo_Symbol" "Chromosome" "Start_Position" [4] "End_Position" "Variant_Classification" "Variant_Type" [7…
Answer: scaffold assembly inro chromosomal assembly using reference genome
by
samuel.a.odonnell
▴ 450
Have a look at ragtag and ragout. I use ragout for smaller assemblies (~20 Mb and less) and ragtag for larger genomes.
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
by
Ram
37k
I've been meaning to work on a Biostars-specific code formatting manual for a while now but the basic is pretty simple: You can use backtic…
Comment: Multiline Fasta To Single Line Fasta
by
Onur
• 0
Thank you it's also worked for me too. Best,
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
by
Estefania
▴ 10
Thanks Ram. Could you point to a manual on how to make the post look like yours? I just copy-pasted my R script and this is how it shows in…
Comment: extracting input files form Seurat
by
rasing02
• 0
Thank you jared.andrews07
Comment: extracting input files form Seurat
by
rasing02
• 0
Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature p…
Comment: Downloading 450k methylation data from GEO
by
GenoMax
125k
I don't think they have provided processed data as a single upload.
Answer: extracting input files form Seurat
by
jared.andrews07
★ 14k
You can get the data behind any of the plots easily enough: ``` p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by…
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