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121,953 results • Page
158 of 2440
Sort: Rank
Rank
Views
Votes
Replies
1
vote
3
replies
1.2k
views
How can we be sure that this module preservation is comparing the same module genes in the two groups?
module-preservation
wgcna
updated 20 months ago by
Ram
45k • written 20 months ago by
Gail
• 0
1
vote
1
reply
1.3k
views
Problem running DeepTMHMM with Docker
Docker
DeepTMHMM
updated 19 months ago by
Alex
• 0 • written 20 months ago by
Elizabeth
▴ 40
0
votes
4
replies
1.4k
views
Help interpreting Samtools Flagstat results
STAR
samtools
RNA-seq
updated 20 months ago by
swbarnes2
15k • written 20 months ago by
ablanchette
• 0
0
votes
0
replies
489
views
Parsing error when using sstacks
stacks
sstacks
updated 20 months ago by
Ram
45k • written 20 months ago by
Hayler Edu
▴ 40
1
vote
3
replies
926
views
Annotate wormbase genes
RNA-seq
19 months ago by
leranwangcs
▴ 150
0
votes
3
replies
1.0k
views
Its possible to merge GTF files from different genome versions so I can assing the seqnames from one ot another
Genome
GTF
updated 20 months ago by
Ram
45k • written 20 months ago by
Nicolas
• 0
4
votes
1
reply
1.1k
views
Clustering sequences in a pandas dataframe
pandas
python
clustering
updated 20 months ago by
dthorbur
★ 3.1k • written 20 months ago by
ba2so
• 0
4
votes
8
replies
1.5k
views
GCP Snakemake
snakemake
GCP
updated 20 months ago by
Ram
45k • written 20 months ago by
Fadwa
▴ 10
23
votes
12
replies
33k
views
9 follow
Extract Alignment From Very Large Bam File
bam
updated 20 months ago by
Ram
45k • written 13.3 years ago by
Plantae
▴ 390
0
votes
1
reply
1.0k
views
GATK-Pathseq validation
gatk
updated 20 months ago by
Ram
45k • written 2.6 years ago by
annaA
▴ 10
2
votes
3
replies
1.0k
views
VEP classifies exonic variants as downstream
ensembl
vep
updated 20 months ago by
colindaven
8.0k • written 20 months ago by
tvrlisml
▴ 20
0
votes
0
replies
433
views
unusual alignment rates for IgG and H3K27me3 in cuttag
bowtie2
cuttag
20 months ago by
david
• 0
0
votes
3
replies
1.4k
views
WGBS data presentation
WGBS
R
updated 20 months ago by
Binte.farooq
▴ 20 • written 3.5 years ago by
sinha.puja
▴ 20
2
votes
6
replies
2.4k
views
How to visualize multiple bacterial genomes with circos?
atlas
genome
visualization
updated 20 months ago by
mathavanbioinfo
▴ 80 • written 20 months ago by
marongiu.luigi
▴ 760
1
vote
1
reply
610
views
Differential Abundance between samples
Differential-Abundance
Mass-Spectrometry
updated 20 months ago by
i.sudbery
22k • written 20 months ago by
catfishtom
• 0
2
votes
4
replies
1.3k
views
Suggestions for a simpler solution for collecting snakemake rule output in a text file for use in another rule?
snakemake
20 months ago by
a.v.vliet
• 0
0
votes
6
replies
1.1k
views
Doubt about fpkm file
FPKM
RNA-seq
updated 20 months ago by
ATpoint
89k • written 20 months ago by
mounavisirekolam
• 0
2
votes
2
replies
664
views
Errors from REST and Browser for specific HOGS?
OMA
20 months ago by
Andrew
▴ 20
0
votes
6
replies
1.6k
views
Normal number of variants to lose during liftover: GRCh38 to hg19
liftover
1000genome
CrossMap
updated 20 months ago by
Giulio Genovese
▴ 630 • written 20 months ago by
JourneyToAbyss
▴ 250
0
votes
1
reply
658
views
WGCNA - higher number of modules
WGCNA
updated 11 months ago by
allingt
▴ 40 • written 20 months ago by
marina.wakid
▴ 10
0
votes
1
reply
811
views
mitch analysis report priority by standard deviation
mitch
standard_deviation
updated 20 months ago by
mark.ziemann
★ 2.0k • written 2.8 years ago by
Amr
▴ 180
1
vote
2
replies
871
views
How to get differntial Protein expression from protein abundance?
Proteomics
protein
DEPs
Abundance
updated 11 months ago by
Saadyeh
• 0 • written 20 months ago by
Omar
• 0
2
votes
2
replies
1.0k
views
Trouble Running VEP in Conda Environment Due to Perl DBD::mysql Error
perl
conda
VEP
updated 20 months ago by
Ram
45k • written 20 months ago by
qiuting
▴ 20
1
vote
6
replies
1.6k
views
RNAseq analysis: how to add new gene into an existing worm based reference
RNA-seq
updated 20 months ago by
jkim
▴ 220 • written 20 months ago by
leranwangcs
▴ 150
0
votes
7
replies
1.4k
views
Iterate through Seurat object to add patient information
R
Seurat
updated 20 months ago by
Ram
45k • written 20 months ago by
kousi31
▴ 100
9
votes
5
replies
1.3k
views
Annotation of Complex Heatmap
complexheatmap
20 months ago by
abiuma
▴ 30
1
vote
5
replies
1.8k
views
Querying nr_clustered database using BLAST REST API?
blast
clustered
updated 20 months ago by
GenoMax
154k • written 20 months ago by
cmdcolin
★ 4.3k
0
votes
1
reply
501
views
how to determine the percentage of reads after sequencing?
metagenomic
sequencing
updated 20 months ago by
GenoMax
154k • written 20 months ago by
Ales
• 0
0
votes
1
reply
491
views
Error in GDCRNATools
GDCRNATools
ceRNA
RNA-seq
20 months ago by
Matvii Mykhailichenko
• 0
2
votes
3
replies
966
views
WGCNA Soft Power Problem
normalization
wgcna
RNA-seq
DESeq2
updated 20 months ago by
LChart
5.1k • written 20 months ago by
Ömür Koray
▴ 10
0
votes
0
replies
617
views
WGCNA module preservation
module-preservation
wgcna
updated 20 months ago by
Ram
45k • written 20 months ago by
Gail
• 0
0
votes
2
replies
806
views
Docker container not running (or stopping immediately)
docker
Hi-C
updated 20 months ago by
Eijy Nagai
▴ 90 • written 20 months ago by
Panagiotis
• 0
3
votes
2
replies
787
views
Alternatives to Mummer3 for linux?
alignmemt
sequences
aligner
updated 20 months ago by
Dave Carlson
★ 2.2k • written 20 months ago by
marongiu.luigi
▴ 760
1
vote
1
reply
489
views
filtering gene sets when performing scRNAseq data analysis
scRNA-seq
updated 20 months ago by
Ram
45k • written 20 months ago by
Sara
▴ 280
0
votes
1
reply
552
views
Importing read pairs from BAM with specific R1 and R2 start/end positions for pair
Rsamtools
updated 20 months ago by
Pierre Lindenbaum
166k • written 20 months ago by
Emily Wasson
▴ 30
0
votes
0
replies
777
views
how convert a GraphPad PRISM parameters in R code?
R
statistics
regression
20 months ago by
star
▴ 350
1
vote
1
reply
658
views
Genome Analysis Insights: BUSCO Evaluation of Repetitive Elements and Ploidy Level in Crocus sativus"
coverage
ploidy
complex-genome
BUSCO
updated 20 months ago by
Ram
45k • written 20 months ago by
mathavanbioinfo
▴ 80
2
votes
4
replies
1.7k
views
Manhattan Plot
qqman
pcadapt
manhattan
GWAS
updated 20 months ago by
dthorbur
★ 3.1k • written 20 months ago by
Emily
• 0
0
votes
2
replies
875
views
Need some help to develop some python code to analyze kmer data
Python
R
20 months ago by
schlogl
▴ 180
2
votes
5
replies
1.4k
views
Why do I get DE non-polyadenylated genes in a RNAseq with PoliA library?
lncRNA
PoliA
DGE
RNAseq
DESeq2
updated 20 months ago by
i.sudbery
22k • written 20 months ago by
ev97
▴ 40
1
vote
1
reply
568
views
Analysis of .csv data in R software
tabe
csv
software
data
R
updated 20 months ago by
ATpoint
89k • written 20 months ago by
martta95
▴ 10
1
vote
3
replies
2.4k
views
GOSeq gene ontology enrichment analysis in rice
goseq
R
updated 20 months ago by
i.sudbery
22k • written 5.3 years ago by
Bioinfonext
▴ 480
0
votes
1
reply
648
views
Batch correction for eQTL analysis
batch
eqtl
batch-correction
batch-effect
updated 17 months ago by
Ram
45k • written 20 months ago by
maximal_life
▴ 20
1
vote
1
reply
661
views
how convert hg19 to hg38
hg19
hg38
updated 20 months ago by
Pierre Lindenbaum
166k • written 20 months ago by
arwa.ahmad95
• 0
0
votes
0
replies
348
views
Obtain expression data for the specific genes on integrated seurat project
scRNA-seq
Seurat
20 months ago by
gdfsnkfns
• 0
6
votes
4
replies
1.3k
views
Trouble with samtools view not filtering specified regions of bam file
bam
samtools
updated 20 months ago by
Istvan Albert
103k • written 20 months ago by
haydenshinn
• 0
0
votes
0
replies
857
views
Tool:
Get `BPCells` with Bioconductor workflow
single
cell
BPCells
20 months ago by
Yun
▴ 70
7
votes
15
replies
2.7k
views
6 follow
I would like to exclude rRNA in RSEM and quantify other genes.
STAR
RNA-seq
RSEM
updated 20 months ago by
dsull
★ 7.7k • written 20 months ago by
Apprentice
▴ 190
4
votes
7
replies
2.9k
views
Help in choosing the right metric for ranking genes in fgsea
FGSEA
GSEA
20 months ago by
Ngrin
• 0
1
vote
9
replies
1.5k
views
Approach for multi species comparative transcriptomics and differential expression analyses
DE
RNA-seq
transcriptomics
updated 20 months ago by
dthorbur
★ 3.1k • written 20 months ago by
fish_enthusiast
• 0
121,953 results • Page
158 of 2440
Recent Votes
Comment: Looking to learn practical bioinformatics
Answer: MAPQ algorithms of Giraffe
Answer: MAPQ algorithms of Giraffe
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Comment: HIV : gtf or gff annotation
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Comment: Slam-Seq Conversion Rate per Read
by
michael.ante
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Try to switch to percentage view of this graph. Stacked bar charts with different heights can sometimes be misleading.
Comment: Functional prediction for proteins of bacteria.
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Biochemical changes
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
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Sorry about that. It's when I align the paired reads together like the left and righ, they should align with common sequence at some ends, …
Answer: Dictys refuses to use CUDA supported pytorch during installation
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I fixed my problem by ``` conda create -y -p /project/spott/zwjiang/conda_envs/dictys_gpu -c conda-forge python=3.9 mamba conda activat…
Comment: HIV : gtf or gff annotation
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Thank you for your response! We have just posted the full preprint to BioRxiv (https://www.biorxiv.org/content/10.1101/2025.09.24.675449v1)…
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Just adding some detail here that may help draw some connections with other posts, I did a bunch of sleuthing with selectively trimming dif…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
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It's a little unclear what you mean by "I was able to use wgsim, but when I tried aligning the paired-reads, it's not aligning together."
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89k
Just to be sure: You ssh into a remote server, correct? Die you setup the conda environment on your local machine or the remote? Must be th…
Answer: pySCENIC aucell matrix is all 0s
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Tripfantasy
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Sorry to those of you having the same issue. I haven't been on here in quite some time! I've documented my fix on pySCENIC's github page be…
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anovak
▴ 180
I think this is still not quite right because I think your tags need to be tab-separated in the output to really be parseable, and here the…
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`vg giraffe` does not use the exact same MAPQ algorithm as bwa-mem. However, its mapping qualities are still meant to be Phred-scale probab…
Comment: using packages with conda
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raquel
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Yes, I'm using SSH session
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
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Mensur Dlakic
★ 30k
I think only a fraction of sequencing errors can be specified. If a mix of a reference and a mutated genome is included, setting sequencing…
Comment: using packages with conda
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89k
Cannot reproduce. Is this run via some sort of server/HPC/scheduler/something?
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89k
Seriously, an ordinary limma-voom analysis between two groups is as little of 5 lines of code. Please read the limma user guide which cover…
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